There's this blog post:
http://blogs.adobe.com/flashplayer/2014/11/adobe-air-and-android-5-0.html
Short version is: Google will do a fix in the OS, in the meantime you can make apps with a 2048-RSA certificate, and those will work ok. The article has link to a patched ADT.jar file that defaults to 2048 instead of 1024. If you're using Flash Pro you can already select 2048 when making a certificate.
One thing I haven't tested yet, but will soon, is whether you can update an existing app that used 1024-RSA to one that uses 2048-RSA. Normally Google reject updates that don't use the same certificate as the previous version.