Frequently, when I have a Foundry mission in my sidebar log, they will vanish from that list, as well as the from the In Progress tab. I am not sure what causes this, but map transfers may be involved.
The mission is still available, if I go to the entry point for the mission, it is there and I can activate it.
This doesn't appear to happen while in the mission, just before it is started.
I've also experienced this, but it has been a long time, say sometime around season 6. I can't remember what the mission was. But it was exactly what chivalrybean describes. I had the mission and could play it, but it didn't appear in the log.
If you need any date or whatnot next time I see it, anything I can do to help, I will.
Thank you. If/when this happens again, try to make a note of what mission was affected, and what happened just before the issue occured. If there was a map transfer, where did you start and where did you end? Anything else you might remember such as were there other missions in the mission tracker, or was the mission set to primary might also be helpful.