Check if there are are mates modified during that mark. Also recalculate the motion study and check if that resolves the issue.
I'm sure there is a very logical explaination as to why this happens. I find it very frustrating and annoying. That said, If the recalculating the motion study doesn't "wipe" the leftovers from the previous run, the only way I have found is to start another study.
If you have several keys set up, you can copy and paste them into the new study.
If there are only two parts it may be quicker to delete them, run the study, then put them back in and run it again.
Thank you both. I ended up deleting the building and re-placing the same one in at the correct spot which solved the issue. When I have time I'll definitley mess around and see if I can fix it.