[UpdateCCTestChecks] Fix --replace-value-regex across RUN lines

Without this patch, llvm/utils/update_cc_test_checks.py fails to
perform `--replace-value-regex` replacements when two RUN lines
produce the same output and use the same single FileCheck prefix.  The
problem is that replacements in a RUN line's output are not performed
until after comparing against previous RUN lines' output, where
replacements have already been performed.  This patch fixes that.

Reviewed By: MaskRay

Differential Revision: https://reviews.llvm.org/D104566