The default @INC paths are normally hardcoded in the perl binary (or are optionally determined relative to the location of the perl binary, if it had been built with -Duserelocatableinc), so they should not change as long as you call the same perl binary. There are various ways to add additional directories, such as using PERL5LIB, the -I commandline switch, or in the scripts themselves via use lib, or by directly manipulating @INC.
Are you sure you're calling the same perl? Are the respective libs still installed after your @INC paths have changed? In what way do they change? What does perl -V show?