Save file pop-up window stops batching progress

My team works collectively and is currently working remotely. We work out of a harddrive and a personalized online database. All Illustrator work is saved to both the online database and to the harddrive. For our quality control process I batch all of the collective ai files to PDFs (this is out of the harddrive). I've noticed (since covid/remoting) that every so often a file will pause the batching process to ask whether said file should be saved before closing. I already have the "Override Action "Save" Commands" for the Destination folder checked. My guess for this issue is that not everyone (a total of 6 people) is using the same Illustrator version. I'm posting this just in case anyone else might have a different idea of what could be causing this window to show or if you agree with my guesstimation.  

Thanks so much, 

Sabrina