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  • By very large number of packages, what sort of number? Might be best to create a new subfile and main.tex that doesn't call any package i.e. no commands or settings, include your custom .cls and then comment out half of the packages, if the error goes away keep reducing the amount of packages you comment out until you find the one causing the issue. Not an expert but I am certain it would be very difficult to diagnose your issue without more details or what packages have been updated, so trial and error it with the comments and locate the specific package first so someone can help better. Commented Aug 28, 2021 at 0:18
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    I've stripped it down to the minimal subfile configuration, as above in the edit, with no luck still. This must be a change in the default behavior of either setspace or subfiles, then. Commented Aug 28, 2021 at 0:51