What about putting com.fantaisiesoftware.purebasicide on the plist of the PB's compiled app, grant perms, delete it, and see what happens?
I'm kidding; that's probably far more risky than the sqlite stuff

PS: talking about this, very strange permission stuff can happen if you duplicate an applescript app and then modify it; it's always better to paste the source code on a brand new Script Debugger doc…
PPS: maybe that can happen also for "duplicate/debug temporary copies" of PB apps (with same bundle id)

Apple…

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