I'm still having trouble with this, I asked in the OpenFL forums but nobody responded.
I converted the p12 file to JKS from the site you suggested (I think I've actually tried it before), and the file was created successfully, the apk compiled fine with the JKS file, but when I try to update the app for Google Play it says "Upload failed
You uploaded an APK that is signed with a different certificate to your previous APKs. You must use the same certificate. Your existing APKs are signed with the certificate(s) with fingerprint(s):"
When I try to sign with the original p12 file, I get the error "Invalid keystore format"
I noticed that for the AIR app, I also had a file called SelfSigned.pfx, which I think was used to create the p12 certificate? Can this have something to do with the problem? I even tried using this pfx file to sign the app, which didn't work either.
Just for the record, I was able to solve the problem by removing the certificate from the apk, and signing it again with the jks certificate, with jarsigner. I basically followed this: http://stackoverflow.com/questions/3267216/can-i-re-sign-an-apk-with-a-different-certificate-than-what-it-came-with So the problem had something to do with how the app was signed, not the certificate.