I do not know exactly what is causing this but I strongly suspect that it relates to another oddity that I have noticed in my tree. That oddity is that many of the relationships seem to have recently flipped from Biological to Unknown, or from Spouse to Unknown, and I am noticing such flipped relationships on every direct ancestor of mine who has disappeared from ThruLines (on Ancestry.com.au) that I have investigated so far.
For example when I go to the profile of my 2nd great grandfather John Murch Stacy, who is missing from ThruLines, and choose Edit > Edit Relationships what I see is below, with red arrows where relationships seem to have flipped, with one of them being to my great grandfather Clement Howard Stacy.
As I find these I fix them, and after a day or two at least two of my missing direct ancestors have reappeared on ThruLines.
I have reported this to Ancestrysupport@ancestry.com.au who responded:
Thank you for contacting Ancestry regarding problems with your
ThruLines not generating properly. We are always sorry to learn our
members had a frustrating experience but are happy to help.
Thank you for reporting this concern. We are currently investigating
this issue. If this is found to be a bug/issue, please note that we
cannot provide any sort of time frame as to when it will be resolved.
We apologize for the inconvenience.