BaseTools: Fix incremental build failure that override file be removed

BaseTools: Fix incremental build failure that override file be removed

Fix a Incremental build failure. The case is: Both A and B package will
include a same .h file, and in the driver's packages section, A
package is listed before B package, so we will use the .h file in the A
package and build success, then we directly delete the .h file in package
A, it cause increment build failure since in the AutoGenTimeStamp file
the .h file in A can't be found.

Cc: Liming Gao <liming.gao@intel.com>
Contributed-under: TianoCore Contribution Agreement 1.0
Signed-off-by: Yonghong Zhu <yonghong.zhu@intel.com>
Reviewed-by: Liming Gao <liming.gao@intel.com>