You will need to provide more detail.
Is the solution hosted on FileMaker Server and everyone uses "Open Remote" to connect to the hosted file?
Where is the data that is getting merged? Is that imported from somewhere?
you did a lot of searching and into-FM-translation for not being a FM user, which is something that has to be corrected asap - the FM community needs homework-doing people like you and I can't start a reply without taking my hat off to that.
Beyond the above, this "merging" or importing looks like working on the - as we FM users call it - "found set".
One (1) record against 12000 records seems being a find which does take place and succeeds (when run on server), or does not, eventually failing by finding all the records (equivalent to not finding at all), on a client.
It can be a global, it can be anything - we need a bit more info, as already posted by wimdecorte.