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I'm a little concerned that I just finished the Freeing Medora quest and the original two log entries (the first, about being sent by the emperor and the second having met Lady Brisienna) have just disappeared. The main quest doesn't have a time limit, does it? All I've got left now is an entry about getting the painting from Wayrest...

Edit - quest related items are gone too, such as an old letter from Prince Lhotun.
Edit 2 - I used an old save to try again and as soon as I spoke to Medora the main quest disappeared.

The first question here is, have you patched your game to the latest version? Because there have been several quest-breaking bugs in earlier releases, e.g. this (fixed in version 1.06.200):

* A major fix has been done to the quest code. This fix would on rare
occasions cause the main story quest to shut down. It also prevented
the curse to be lifted from Daggerfall when you put King Lysandus's
soul to rest. Now when you complete this, a video will play and
Daggerfall will be safe once again.

Turns out it was supposed to happen after all

Ahh, cool