I need to back up my entire DB including one table that's allocated in "Tables -> System Tables". When I try to generate the sql scripts to back up my DB this table isn't mapped in this scripts. Do I need to do something more to map this table to the scripts?
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Creating scripts of objects usually isn't the best backup method.
There shouldn't be any actual tables listed under Tables > System Tables. Those should all be catalog views unless you've hacked the system objects to put one of yours tables in there.