Well, honestly we did not test with cloned source lately, because there is really too much that can go wrong. If the UE build system detects anyhow that the PopcornFX Plugin must be recompile, yes, it will fail, and there is not much that can be done without the Plugin Sources.
The BETA version is free and only for testing purposes (with the UE4 Launcher Engine version). We hope to get the next major version ready next month, with a lot of changes (some breaking changes). So for now, I highly recommend to only “test” the Plugin. If you have already gone past “testing only”, contact us at “ue4 at popcornfx dot com” we’ll see what we can do.