I don't think it's a new problem. For me, Reaper has often forgotten the path to FX Chains, Track Templates, MIDI Note Maps, ...
When Reaper forgets the path to some type of file, I found that I can often make it reset/remember the path by saving a new one of whatever type of file. For example, try saving a new/dummy FX Chain -- hopefully Reaper will reset the path to the correct location, and then remember it when you try to load the FX Chain that you wanted in the first place.
Not an ideal solution, but it works for me ...
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Best Regards, Ernie "lunker" Lundqvist
BDSM (Bad Dog Studio Musicians)
Windows 10 running on Z390 + i7-8700
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