The following KB details information regarding the workaround/behavior for scoped app values in the sys_app table that is overwritten or blanked out after a clone. The KB provides the needed workaround to prevent this behavior from occurring. This only applies to the scenario where the source instance of a clone has installed apps that would exist on the target instance of a clone as a developed app.
Cause for this is still unknown
The simplest workaround to prevent this issue is to create a data preserver and an exclude on the sys_app table on the source instance of the clone. This will ensure that all the data values on the sys_app table are intact after clone.