We have the same problem regarding the performance of the instrumented builds and we also rely on Replays\Gauntlet. The process is time consuming by nature so most teams that use it wait for the end of the project.
For a specific state of the code base, you can merge multiple runs of profiling into the PGD file. You can have multiple replays that you profile and merge. (per level, per game mode…)
As the PGD is generated from a specific state of the code base. It can go stale really quickly as the code is evolving. It’s best to regularly flush the data and do some new profiling sessions to ensure that the data collected still reflect the current behavior of the code.
Martin