This should work. Everything Evolution does is stored in those two
tables, so if you delete them, you are essentially starting from
scratch.
The general use case you describe is a common problem, and it is
something that I would like to address. As an intermediate
workaround, there is a long standing ticket to add some commands to
rebaseline and/or force evolutions in/out of the current baseline.
Yours,
Russ Magee %-)