Issue with modified merging

In !801 (merged) changes were made to the grid submission, which allowed for disabling the merging option. This was to allow the cutflow files to be correctly saved, as we don't have a script that allows merging of both the h5 and the jsons. This seems to however have caused issues, with others no longer being able to submit to the grid. As a result, the change was reverted in !810 (merged). We should figure out why this caused issues. @dguest suggested a possible reason/solution here which we should look into.