BaseTools: Fixed a bug of IgnoreAutoGen

BaseTools: Fixed a bug of IgnoreAutoGen

REF: https://bugzilla.tianocore.org/show_bug.cgi?id=2080
After checking that if the build can't
ignore Autogen due to there is no compelet autogen files,
the build tool need to do a completely Autogen.

This patch is to fix a bug that if AutoGen
can't be skiped, the SkipAutoGen flag
need to set to False

Cc: Liming Gao <liming.gao@intel.com>
Signed-off-by: Bob Feng <bob.c.feng@intel.com>
Reviewed-by: Liming Gao <liming.gao@intel.com>