I'm not sure exactly where and when or if things changed. The essential part of the bug report is that valid APK files are being inconsistently detected as either JAR or ZIP. APK files are always JARs and always ZIPs. If they are not being detected as APK, then JAR would make the most sense, IMHO. I can't see what is causing file to detect those APKs differently.
We ran into this as an issue in diffoscope: https://bugs.debian.org/849638 Oddly enough, the 'tmp' one, which is actually signed with a JAR signature (META-INF/* files) is the one that is being detected as ZIP. The 'unsigned' one which has no signature is detected as ZIP.
