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Hi Ollie,
Unfortunately, the “Source” filter option doesn’t support multiple selection of document libraries yet. The workaround now is to use “select sites” or “this site” to scope all the libraries.
The custom query can only filter items but not the “source”. For this feature limitation, we would suggest you vote this UserVoice: Exclude specific Libraries or files that contain the specified keywords via the highlighted content Web part.. The related team always take popular and useful ideas in this way. Your voice is always very important for us to improve our products and services.
Regards,
Rena