Most likely, your shared object is called
libmyapp.so. This "
lib" prefix is essential for the package manager to locate and install your libraries correctly.
Anyways, the change of file size after upgrading the AGP may be attributed to the build stage when the native libraries are stripped (removing some debug information), which could easily account for a 50% decrease. This strip is performed by the NDK, which must be installed on the build machine even if the APK uses prebuilt libraries. Also, each version of AGP expects a specific version of NDK, and if there is no match, the strip step may be simply skipped.
BR,
Alex