Hi,
I have no idea what I touched or where, but every blog on my site suddenly and simultaneously is unable to publish permalinks and archive pages. Every blog has the same symptom: on the publishing settings page, the "preferred archive" no longer has a drop-down box with choices. It now says, "No archives are active."
Every existing blog now has this problem, regardless of when it was last updated. However, if I created a new blog, it does not have this problem.
Does anyone have any ideas of how to "re-activate" the archives?
(I'm using version 4.2RC3)

Please avoid double (or triple) posting of questions.
Sorry, I am new to the forums, and I thought I had posted my question about 4.2 in the wrong place originally. I didn't realize that the sixapart.com forum and this forum were the same, since I had to create a new login. Thank you for pointing out my error.
Have you looked at your activity log, or perhaps your server logs? You might see something there that can help to restore your publishing preferences.
This happened to me as well and there is absolutely nothing in the activity logs.
I deleted and refreshed so that I got the archives back but there is still the main index not updating as it should. It takes some minutes and the suddenly the main index is updated to. Very strange.
Also there is nothing giving any errors in the server logs.
This started happening after installing to the first MT4.2 RC1 and has not changed despite that I am now on the RC3.
Something did improve after the latest RC3 and that is I got the widget back, the one that shows after log in with MT info with the yellow background.