The problem is preferences migration?.
Same thing happens 65 from 64.

Reproducible: always

Steps To Reproduce:

1. Start Firefox60ESR

2. Setting 'Clear history when Firefox closes'
   2-1. Go to about:preferences#privacy > 'History' section
   2-2. Select Firefox will 'Use custom settings of history' in doropdown Switch on 'Clear history when Firefox closes' and Click on [Settings...] button
   2-4 Switch on all checkboxes and OK

3. Start Nightly68.0a1 with same profile (simulate next ESR upgrade)

4. Go to about:preferences#privacy > 'Cookies and Site Data' section
   --- observe checkbox status of 'Delete cookies and site data when Nightly is closed'

Actual Results:
'Delete cookies and site data when Nightly is closed' is not checked

Expected Results:
'Delete cookies and site data when Nightly is closed' should be checked

Johann or Erica, do you know if this is recoverable at this point, at least for ESR? Can we fix up the migration somehow?

I'll try to figure out what's happening here

Thanks, Erica, I'm a bit swamped, so that would be really appreciated. Let me know if you need any help.

Tentatively assigning to ewright due to comment 2, and marking this P1 since this has the potential to burn users who, at least, assume that their history is being (and will continue to be) wiped at shutdown.

I finally had a chance to look into this and it seems that the "Delete cookies and site data when Nightly is closed" checkbox is new. It is also ruled by a different pref than the relevant checkboxes in the history section. When the upgrade happens, those checkboxes which were checked before remain checked, and those prefs remain on. These two prefs result in almost the same behavior.

So it seems we have some redundancy in the UI, but the user's prefs are not being lost, and cookies will continue to be removed on shutdown. This is not so much a concern only for ESR upgrades, but is a concern having a confusing UI in all cases.

I spoke with UX folks and we could potentially remove the cookies option from the history section, effectively removing the "privacy.clearOnShutdown.cookies" pref and fully replace it with "network.cookie.lifetimePolicy". The difference is that "network.cookie.lifetimePolicy" is currently used to cleanup on shutdown other components such as QuotaManager, localStorage, ServiceWorkers. reference

Oh, now I get what this is about. Yes, those two settings have always been at odds with each other but even more so now that we recently extended what the lifetimePolicy pref does to make it actually clear data on shutdown.

This absolutely needs to be cleaned up at some point, but disentangling this isn't an easy task (AFAICS) and definitely not a regression we need to fix urgently. As Erica said, your cookie clearing on shutdown will continue to work.