That's not really the answer, that's a manual work around. You want something you don't have to baby sit.

Would sure seem to me that removing Replace hsa With has from the Replace text as you type list would prevent hsa from being changed to has.
It does for me in Excel 2010.

Try replacing the part that tells Office what hsa should be replaced with, make the replacement hsa and see if that does it.

Upon further consideration, this might have something to do with the definition of doesn't work.
I believe the auto-correct stuff is part of the overall Office installation on the computer, in which case the auto-correct adjustments would apply to the computer not the file. So the manual intervention would be necessary, at least some of the time.