Empower 3 autoarchive.exe

I have over 40 Empower 3 Personal Workstation systems around the country that we just installed the AutoArchive licenses too. We have them all set to archive "When Needed" as the software manual suggests. The problem we are seeing, is that it's filling up our 4TB Data drives very fast, as well as bogging down our BackupExec servers with multiple copies of the "WHOLE" Project without overwriting the previous copies. This is causing a major issue and for the price of the licenses, I would hope someone had figured out a switch that could be used or something with the autoarchive.exe file to allow the exported project, when modified/new to be writing out but then be overwritten with new data in favor of any recent changes.
Has anyone on these forums ever worked with this and can it be done?
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