Hi Andrew;
I would personally recommend copying the "appeon_workarounds.pbl" to your App's development folder and then add that to your App's library list. This is allows you to choose when your App(s) pick up the newer version, after you install a new MR (Maintenance Release), Revision or major version. Those installs will always replace the libraries (including the appeon_cordova.pbl) in the "C:\inetpub\wwwroot\appeon\developTempFile\appeon_workarounds" folder.
TIP: I always like to "Optimize" the newer appeon_workarounds.pbl when I get an update. That makes the PB compiles and PS deployments run a bit faster.
HTH
Regards ... Chris