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I have ran into this situation before but never understood why it happens.
Sometimes when I run the "Update database structure" I get very many changes on out of the box tables.The generated SQL changes the DB definition of datetime fields.
Edit: This was caused by a change in the option WdbcUseTimeStampWithTZ.
Thanks to @saikatk2447661
I guess the temp table thing is happening because of the check box. Please try after unchecking it.