This is a strange problem and it doesn't sound like you're solving a sane problem. It's easy enough to modify a hash - just remove the stuff that's added.

my %pre_existing_INC;
BEGIN { @pre_existing_INC{ keys %INC } = () }
use Your::Module;
BEGIN { delete @INC{ grep { not exists $pre_existing_INC{$_} } keys %I
+NC } }
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