I see - I take it you have the M8d (dual sim) then.
OK - I can share a little bit, not sure if it's going to be helpful or not.
Your phone storage is divided into partitions, probably around ten or twelve - the bootloader, recovery, radio firmware, the boot/kernel area, the system area, data and of course the sd card is its own deal.
Updates can touch any partition except /data and the internal and external sd cards.
Link2SD points away from /data inside the phone and out to a separate partition on your SD card that you'll create.
So far that's all separate from what an OTA would touch but there's a catch.
The stuff that does the /data swap is in the /system area - and OTA updates tend to check that the /system area is as HTC made it or the update won't happen or worse, will seriously break something. Ditto for other partitions.
That's why you have to be unrooted for an OTA to work right - root modifies /system.
At minimum I would guess that you're going to need a way to root and unroot, possibly be able to go back and forth between stock and custom recovery (so you can root), and somehow be able to reverse the Link2SD mods along with unrooting.
Wish I could help with the mechanics but I don't know this stuff well enough.
Pretty sure that's the stuff to be looking out for though.