mysql workbench migration changed my database. Can I trust it?
Seems you've found a bug in migration wizard, I follow your description and I was able to repeat issue on my machine. Can you please fill bug report at bugs.mysql.com? Appreciate. We'll do our best to fix that isse.
As workaround you can try this way - use Data Export to export only structure of your database. Run exported stricpt on target server. Then run migration wizard normally, but skip create target schema step. Let me know if that works for you.