Increase in number of temp files being generated after increasing checkpoint_timeout
Using temp files is not necessarily a bad thing.  They are nothing to worry about unless the queries that have started using them have gotten slower, or the amount of them that exist simultaneously is threatening to fill up your storage.  The change to autovacuum setting is more likely to be the cause than the change to the checkpoint setting.

What lead you to make these changes in the first place?  That could provide a clue.