The possibility is remote but when running on an SD card, files yuo’ve deleted suddenly reappearing on a reboot can be a sign of a failing SD card.
Also, with a standard openHABian install with zram configured, how you restart matters. Any changes you’ve made to the config only exist in RAM. You must shutdown the machine normally for any changes you’ve made to get saved out to the SD card. If you just pull the power all your chages get lost.
Do you mean $OH_CONF/services which has files to config things like installed bindings and such? Yes that folder is still there and config files in there are still used. And any config files in there will take precedence over anything you do through the UI. You should use one or the other, not both.
addons.cfg is the file to look at in that folder if you suspect you ahve an old version of this file hanging around.