I had this issue when my flask simple app kept failing the next day it was started.
It kept giving the error "MySQL server has gone away".
I tried a couple of things like, starting the mysql session for every request instead of for each flask process (app-wide). But apparently flask doesn't like that.
At least not when using flaskext.mysql's MySQL.
I think I didn't have much luck trying to change the timeout on flask either, as this module just didn't let me.
I could have changed the module to use mysql, but I didn't have much time to finish the damn thing, so in the end I just set a cron job to access the mysql select query using page every 10 min or so. Ugly, but simple workaround.
It was like
curl -k https://localhost/some_app/index.html
every 10m.
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