For the actual storage of Sage 100 itself, I've never tried Windows built-in dedupe tools (since 2012?) but I can't imagine it would go well with transactional files.
However, most of the backup tools that we've used over the past few years (Datto, StorageCraft, Altaro, Veeam, etc) all perform deduping on the backup target-side and we'll usually get an 8-10x compression with the MAS_* folders. Combine that with some sort of Full + Incremental backup strategy, and they should be covered pretty well.
It sounds like they're in a tough situation since any recovery event would be an absolute time suck. If I had my IT Architect hat on (and sufficient budget), I'd probably have some sort of time-delayed (~30 minutes) VM-server-level replication going on with frequent server-data-level snapshots. So that if the server completely blew up, you'd be up and running immediately with < 30 minutes data loss, however, that would require double the licenses and resources, especially storage.
Not sure if I really helped you or not, but good luck, and let us know how it goes! :)
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Steve Iwanowski, NextStep Technology Advisors, aka DSD Lancaster PA ¯\_(ツ)_/¯
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