This answer is mostly anecdotal and hearsay based, so take it with a grain of salt if somebody with experimental evidence shows up.
There was at one point a pretty far reaching pilot allowing deprecation of nearly anything in managed packages. It was, from the accounts I heard, a pretty bad failure and had the capability of breaking things very badly. However the deprecated attribute from the pilot was added to all (managed?) metadata during the pilot (although it couldn't be set to true unless you were in the pilot).
Sometime in the last year or so I think they finally put the final nail in the coffin for the pilot in it's initial form, and removed the metadata from object definitions. Since you're using version control and didn't update the metadata yourself you're likely finding the deprecated element removed the next time you go to make a material change to the object.
This happened to me, and it was something like 6 months of this slow motion process before the last of the deprecated fields was finally out of version control.
It should stay gone at this point.