We should look at adding a migration handler to the patch which will apply fixes retro-actively without requiring the player to enter NG+ to take advantage of the changes.
A running list of known script we will need to migrate is shown below:
Constellation companions no longer have the wrong dialogue in NG+ after completing "Foreknowledge". [qf_mq204_002c6d74] #164
The number of undiscovered temples shown in the UI will now match how many are actually undiscovered. [starborntemplequestscript] #231
The doors to Coe Estate will now properly unlock on entering NG+ [qf_mq401_001dc45e] #370
The variable indicating that you had previously met Lillian during Sam Coe's questline will now be properly set. [qf_mq401_001dc45e] #373 (Possibly not fixable as in NG+ the only way to know if the player has met Lillian is to check this value!)
The variable indicating that you had previously completed Sam Coe's commitment questline will now be properly set. [qf_com_quest_samcoe_commitme_000df7ad] #372 (Possibly not fixable as in NG+ the only way to know if the player has committed to Sam is to check this value!)
Cora Coe will now correctly join the player's crew when Sam is recruited as a companion or crew member in NG+ [qf_mq401_001dc45e] #369
Fixed a potential softlock issue when arriving in a variant universe in NG+ [mq401questscript] #314