I've used a portable HW rig in our church on a number of occasions (and at one point I even cobbled together streaming HW via zoom to church when I needed to quarantine but Mass had to go on...). I've never had any issues. That said, I'm tech savvy and have been using HW for a long time.

I recently visited a bespoke HW installation in a church down in indianapolis that was completely built around HW. Even as a seasoned user, I found myself very disoriented whenever a new sampleset was loaded with which I was not familiar.

If you go this route, (and I'm not saying you should not; I've mulled over the idea for our church too) here's what I would suggest:

1.) pick a dry or semi-dry sampleset.
2.) voice the instrument to the room! the Indy installation was interesting because some samplesets had been meticulously voiced for hours, and others had not, and you could easily tell the difference. The dry sets that were meticulously voiced sounded the most realistic.
3.) limit yourself to a single sampleset (or two at most). Having a panoply of choices will only muddy the waters. It's really tempting to just throw a bunch of samplesets on the computer and pick them at a whim. I believe the best result would be selecting a single instrument (just as a real organ would dictate) and learning to use it as a single instrument.
4.) I suspect subs will be averse to this as an option unless you have it set up as a dedicated system, that essentially never turns off or doesn't require them to boot up computers and load samplesets. If they haven't used HW before, they will be utterly lost. Conversely, if the computer boots up and HW auto loads the first and only sampleset, you shouldn't have too many problems.
5A) you'll want a physical combination system. Trying to wrangle with HW's in-built combination action is not live-service-friendly. I had some issues in Indy when I wanted to use the sequencer but it was getting out of sync with pistons. Conversely, on my home instrument (Johannus) I have physical stops mapped to virtual ones, and then I use the Johannus's in-built capture system of 8 levels. Physical pistons trigger physical stops which activate their virtual counterparts. In this way I can completely ignore the computer if I want to.
5B) if you create a console with physical stops I doubt you'll have any major issues for subs (or yourself, for that matter). I find that in the heat of the moment it is difficult to mess with virtual stops. It's very easy to grab a stop knob or punch a rocker tab.

So to recap:
Get a physical console with physical controls; wed those physical stops to a single, well-voiced (dry) sampleset. Then you can pretend that there's nothing irregular about the organ, just as if it were a Rodgers/Walker/Allen etc.

I have been using Hauptwerk software for some time (the old ver 4 when it used to be free with some limitations), as well as the free GrandOrgue and Jorgan. I have a collection of samplesets, but prefer the French organs. I use it with a fast desktop type computer on the floor devoted only for this purpose and have a touch screen monitor hovering over the console for choosing the stops/registrations quickly. The sound is connected to an amplified good quality speaker system including a 18" subwoofer for those 32 ft stops, and I also use an outboard reverb for those dry samples. My console is a 2 manual with AGO pedal board, a Rodgers 525. It does not matter what console you use as long as it has MIDI which connects to the computer that runs the software. It is a practice organ in my living room, but can easily be adapted to a church, and it sounds great, way better than the original sounds from the Rodgers console.

The software (all 3) is easy to use once set up. But setting it up can be difficult if one is not computer savvy.

Rarely does a note "stick" on Haupwerk, in which case there is an emergency menu item to stop it. This is better than on a real pipe organ which in many cases one would have to turn off the blower to stop it.

Charles:
If you are up to it, there are MIDI interface retrofit kits available that will convert an existing non-MIDI electronic organ to MIDI output. It would mean disconnecting (and scrapping) everything inside the organ except for the keyboards, stops/pistons, and crescendo/expression pedals. These would need to be wired one note at a time to the conversion kit. It is very time consuming, but not really hard to do at all.

Hauptwerk actually sells their own kind of MIDI interface retrofit module, but one can find other, better, MIDI interface retrofits elsewhere, such as the USA made modules from DTS Midi Systems.

If you actually want to build your own conversion electronics, you would need to be quite a bit electronics savvy, but there is plenty of information on the Internet for this if you are daring. Here is an example:

https://www.instructables.com/Adding-MIDI-to-Old-Home-Organs/

Sarah, another thought: large, adequate subwoofers are a must. It doesn't matter how nice the manuals sound, the organ will seem anemic if there is not sufficient grounding in the pedal division. The indy organ had two large bespoke subwoofers, but they weren't quite balanced properly (I chalk this up to voicing). I found the pedal aspect wanting.

I've played many digitals of various builds from fancy allens replete with pipe facades, rodgers, hybrids, $250k Walkers and even a large well-known M&O; the thing that perhaps most jumped out at me when comparing these organs was that the most realistic of them had the most authentic bass and authority in the pedal division. In this case, it was a large 4m Walker in a 1000 seat church. The subwoofer was literally larger than my refrigerator. It made all the difference in the world, though. I don't make this observation as some sort of bass head... just that real pipe organs are grounded by sufficient pedal divisions that you feel as much as hear. For the illusion to be complete, this needs careful consideration.

Francis, I don't mean to offend, but let's not trot out this tired old trope yet again. Let us spare this thread a pointless war. Not every parish can afford (or even physically house) a pipe organ.

Sorry, Serviam... No offense taken.

I couldn't resist the the phrase of 'illusion to be complete'... I guess I was baited...

OTOH

I have a Hauptwerk setup... I don't think I would ever put it in a church because it is very difficult to understand and utilize, especially for other organists who would sub, and making it acceptable as a substitute to an Allen or Rodgers (acoustically) would be quite difficult and could be very costly.

This is not that much more money and is a much better choice.

https://www.organclearinghouse.com/organs-for-sale#/3068-detlef-kleuker-newark-nj

or

https://www.organclearinghouse.com/organs-for-sale#/3061-casavant-asheville-nc

We seem to be forgetting that the OP was asking about using HW in a church installation.

A parish I play at (side job, not full time) had an older Rodgers that died and couldn't be fixed (it was never installed properly to begin with). A pipe organ was ruled out due to both space constraints and budget. We considered a Hauptwerk installation, but...
I'm not that tech savvy and just wanted something that would turn on an play and there are multiple organists who play at this church since they don't have a full time organist.

We decided on an Allen and I'm very happy with that decision.

Sure, I would prefer a pipe organ if it were feasible. I might consider Hauptwek for a home installation, but I think Allen is the safer option for a parish installation.

I think Allen is the safer option for a parish installation.

I think this is technically true (the same is true for other mainstream builders) only insofar as you can have a professional come service the instrument if there's ever an issue.

The fact of the matter is, there are professional "dealers" (for lack of a better term) who are doing church installations of HW now, that include remote trouble shooting and professional installation and service. If you want to put a windows 10 touch screen on top of the console and hope for the best, I'd look elsewhere. But if you engage one of these companies who do this professionally for churches, they will be mounting computers with baked in redundancy in server racks, etc. etc. and they will be quite stable. It all depends on how home-brew or professional you decide to make it. The installation I tried in Indy had 48 independent channels, 3 subs, computers mounted in server racks in a room, a remote connection to the console, etc. I suspect it will serve the parish for a very long time and they accomplished the project for a fraction of what a similarly-equipped Rodgers or Allen would have cost. But it also took a lot of legwork from the incumbent to get the project to where it is today.

Keep us posted. I am going to have to make a similar decision with my home practice instrument - fix the Rodgers, buy an Allen, or go Hauptwerk. I would like to know how this turns out for you.

Sounds amazing! I want to buy the sheet music, too.