Seems it is needed to customize your installation to RaspAP (not the other way around) because it occupies your setup. There ist a FAQ from RaspAP. One point is:
My custom rc.local/networking configuration/wpa configuration is gone!
Currently, RaspAP generates a few of its own files so that it starts with a known configuration. Your custom configurations haven't been lost however, they've been moved to the backups directory in /etc/raspap/backups.
Feel free to SSH in to restore those files to their rightful position, however, you may need to ensure that the RaspAP modifications are applied to your own custom configurations.