This one is new in Domino 8.5.1 and later, but I just came across it the other day.
You can use COMPACT_FILTER= followed by a comma (or semi colon) separated list of databases to exclude from Compact when it is run server wide or against a specific directory
Technote
Great stuff, Mitch! Thanks for sharing 🙂
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if the NSF file is in a subfolder or a linked folder, do I have to include the whole path of the file or simply type the filname?
i.e ndata/filename.nsf