I am looking to reinitialize my NAS and start fresh, but I have one big raid5 array with only user data. What would happen if I just unplug these 3 disks, fully reinitialize the NAS, set it up fresh, and then put the 3 disks back in?
Will it be able to keep the raid5 array?
Hi and welcome to the forum. 
The NAS config is kept on those disks. If you remove them, and reinstall then later, the NAS config will be the same.
Sorry I should clarify, I have a secondary raid with NVME disks in my NAS which contains the configs/OS.
The OS is always on all internal drives, same with the config (see md9 and md13)
Backup your data, then reinitialize the NAS with all drives plugged in. Then setup your NAS and then restore user data from the backups.
HTH 
With your system now on it’s own NVMe pool/volume different than your raid5 pool, safely detach the raid5 pool (I’d then unplug raid5 drives for caution during QTS/hero reinit)… GUI → storageNsnapshots->select/highlight raid 5 pool → Manage → Action button pull down select ‘safely detach’. After satisfied with system reinit/rebuild work, replace Raid5 disks and to recover… GUI ->StorageNsnaps-> Disks/vjbod → triple vertical dots upper right pull down → Recovery → Attach and Recover POOL. (may need to recreate nongeneric access permissions in ‘shared folders’).
I do this process for firmware upgrade on all capable qnaps (can’t safely detach a pool if it holds system volume (“volname(SYS)” flagged in volume list display in StorageNsnaps)) so I can upgrade and then test with ‘trash disks’ and see stability before considering exposing my data disks to the new firmware.
PS - TOTALLY dislike this new forum app compared to the old one. Shouldn’t have to deal with an inferior tool/structure to get qnap to actually look at forum. I suspect QNAP committed to view it convinced it will be used a lot less, certainly by me. PLEASE get a much better application or go back to the old forum!!! In any event other than fallback, do something to make old one viewable in its current format for a distant indefinite future.
I cannot see QNAP just droping discourse after spending much time developing it to what it is now. The old board with phpbb and plugins was horrible to maintain. I had several requests to move to xenForo due to the phpbb being unsatisfactory with spam management, and being laggy and timeouts. I just hope the platform that Discourse is on can handle the load.
Unfortunately we have no choice in what Qnap decide. It is what it is. I just hope they developed it better than the layout it is at present.
qnap - wheres the dark mode 