I am able to reproduce this when Enigmail is the only add-on enabled.
I am able to reproduce this both with the Ubuntu 18.04 build of Thunderbird 52.7.0 and with the official build from thunderbird.net. As noted above, I no longer have to go through the Manage identities part to reproduce this. It happens if I go straight to the OpenPGP page for one of my accounts, change the draft encryption setting, and try to OK it.
The Send Later who originally reported this issue to me now reports (as of April 21), "Now when I click replied messages in my drafts folder that are awaiting to be sent later, another "Re:" is prepended, so the subjects become "Re: Re:"…"
"Re:" prefix on subject line disappears when editing encrypted, saved draft
Can't edit account OpenPGP settings
Actually, now I'm able to reproduce this issue without doing steps 2-4, i.e., just steps 1, 5, and 6 produce the error shown above and the dialog refuses to go away. But I was definitely able to make the dialog go away at one point, so the problem appears to only happens sometimes, I can't figure out the circumstances in which it happens. I thought it was only after managing identities as I described in the initial report, but that's not right.
Can't edit account OpenPGP settings after editing identity OpenPGP settings
Link to "unresolved bugs" search on enigmail.net should exclude closed, duplicate bugs