In my opinion this is the worst option and should be markt as very very dangerous in distributed setups.
In my system here there is one extra folder “/activiation”.
The replication changes and status files are ok. With these files your master knows where needs a config pushed and activated.
The Only thing what you can do now is that you pay attention to your web server log at the time of the activation of a single site. Please try the sites one by one not all together to get a better picture what happens.