I am not quite sure I fully understand your scenario here.
Are you saying that the custom action changed, for instance, its' "Execution Time" from "When the system is being modified (deferred)" to "Immediately" from opening the 15.6 project in Advanced Installer 18.2?
If that is the case, I have run some tests on my end and everything worked as expected - no properties were changed during the process.
Could you please create a sample project that reproduces this and forward it to me so I can further investigate this?