When ACADE inserts a footprint, it actually scans the block for attributes, too see whether it needs to add anything. If the attributes in your legacy blocks are properly named, there should be no issues. At least, not with the shifting footprint thing.
As for using the schematic align command on footprints...I want to say you shouldn't, but I can't think of a good reason to. I'm certain that all this command does is align entities by their insertion point, regardless of what they are. Note that it will align a signal arrow with a wire number. The only thing those two things have in common is, they're blocks. So, insertion point.
Now, with your added information, I'm beginning to suspect your library locations.
By default, these are installed on the local hard drive. When you edit the blocks and fix them, those changes would only be stored on your machine. If another user were to then run an update, it could force the change. (Explained below)
How do you manage your installs for multiple users? Do you share the AeData folder on your network? If not, then IMHO you should. Not doing so could be the reason for your issue here. If you are set up with a shared AeData folder, then I would check to make sure each workstation is pointing to the correct one, and/or that its local AeData folder has been renamed.
Is everybody on the same version of ACADE?
I think this is the most likely root cause for your issue so far.
Now, as to why an update may cause a block to change. This assumes that you and another user are pointing to different libraries, and/or different footprint lookup databases.
Bear with me a moment: I've noticed that during certain update functions, what ACADE actually seems to be doing is not updating per se, but rather deleting the old block and reinserting it with the new info. Keep that in mind...
Let's say you fix a block. As is correct, you have purged the old block definition from the drawing before reinserting the edited block.
Now let's say another user opens that drawing. Runs an update. When ACADE kills/rebuilds the block, perhaps it is looking at the local AeData folder during the reinsertion, rather than the block definition that's already in the drawing (that you fixed earlier). If that's the case, it would explain why an update could shift a footprint.
That's my best wild guess, at any rate.
You seem to be in a situation I've seen before, and it sounds like you're doing all the right things. Clean up the old blocks, maintain connectivity between schematics and layouts, find ways to keep things familiar for the others while easing them into new workflows. This problem seems odd - and to be clear, ACADE has its fair share of quirks - but I think it's fixable.
Jim

Jim Seefeldt
Electrical Engineering Technician