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Just curious,I don't follow the update progress very often and I notest two versions in my pcsx2 folder once I used my updater

Is it just how the buildbot does them now or do we have two versions now?

It's a temporary measure, there are some issues in handling AVX2 and SSE4 modes in one exe which needs work, so until we sort that out there's 2 executables. Hopefully we can sort it out before the next release.