Upgrading CPP and losing member answers

Hello. I am upgrading our install of CPP from 1.2.5.1 to 1.2.6.7.

Our site is a multisite network, and we have thousands of users. However, when testing in our development environment, I am experiencing multiple issues.

1 - Users registered for a course with 1.2.5.1 suddenly have no courses registered or completed.
2 - Users who have submitted answers for part of a course now find that their sessions are incomplete:
- the backend shows all their answers
- if they retake that session and cycle thru answers, there is no change
- however, if they update an answer, then CPP records that as being complete. But the student would have to update *every* answer. Perhaps this has something to do with a date submitted check? Backend shows answers submitted a few months ago, but those arent recognized by 1267.
3 - we have some courses (all actually), with mandatory elements. However, upon testing the upgrade, those units are no longer mandatory! It appears to be random. For example, unit 1 and unit 3 successfully lock out their following units, but 2, 4, and 5 do not lock out the following unit. If I reorder 1 and 3, they will lock out their new following units.

I realize this is a lot and may be confusing. Please let me know if I need to elaborate anything, or send you access to my site. Thank you!