You started again from delete.fpm, added entities and the error reappeared, and yet there were multiple occurrences of the entity type which eventually caused the error? Am I understanding correctly?
EDIT
I just opened up delete.fpm in HxD and it doesn't generate your error 'coz there aren't any entities in it, so my earlier posted question is pointless
, (I wish there was a forum facility to simply delete one's old posts).
Is there a copy of the fpm that generates the error available?
As I understand the fpm, there's one record for each entity type in the map and one record for each instance in the map, but I would have expected the original file location to be stored with the type record rather than the instance record.
If, in fact the latter is true, then your error can be explained by a corruption of the in-memory map which only affected that one instance in such a way that internal file structures were not compromised - so when you saved your map you saved the corruption. If that happened then identifying the underlying cause of the corruption would be nigh-on impossible, and quite possibly limited to whatever else was going on in your pc at the time.
I'd love to have a look at the broken fpm, just to satisfy my curiosity
You can't teach an old dog.