In any case where a single user has two machines, much care has to be taken that: every time a send and receive is done on the one computer, it is also done on the other. So leave work, do S/R, come home do S/R.
Paratext might try to be smart about this if that is not what is being done, but to me, it is the primary suspect in this case.
And of course, a code should never be shared between two users, but you already know this…