I had this problem upgrading from 2.6 to 2.9.11. Solved by resaving the forms using urls with the old form’s IDs like:
/wp-admin/admin.php?page=ninja-forms&tab=builder&form_id=1
/wp-admin/admin.php?page=ninja-forms&tab=builder&form_id=2
Still have one problem where new submissions in these forms starts with index #1 and ends up at the end of the list. Don’t think that will be an issue for me but if anyone has a solution/suggestion for fix I would appreciate it.