Unexpected shutdowns (e.g. OS crash) will cause config.json to become corrupted. I believe this is because Mailspring keeps it open for R/W axis, so it becomes corrupted if Mailspring doesn’t shut down properly.
The client should behave in a way that is robust against this issue.
It seems this issue is related to the ones mentioned by @ccc5vd. This happened before on Nylas, detailed here and the fix was reviewed by @bengotow, here.
If this is a regression from Nylas, propagated to Mailspring, maybe we already have a solution.