By design. Losing all rules because of sync snafu out of control of uMatrix is the absolute worst case. Importing/merging manually will prevent such disaster.
Well, if it would be incremental (passing changelists of rule additions and deletions rather than state snapshots), then any serious data loss should be very unlikely. And if deletion log records would contain the deleted records and prunned only after a short while, things could be even rolled back.
As I get it, it would require significant changes to the code, though.
As I get it, it would require significant changes to the code, though.