Ok here a bit more explanation on how target settings work, in this example for Security Provider.
Initially, when you create a new security provider, a single set of settings is used for all targets.
However if you go to a specific target and make some changes - then this target retains its own settings and no global settings are used but the ones you specified.
This force you that if you have changed again settings on the development target, you have to reapply manually those settings to the other changed targets.
In your case you probably had initially some security provider settings (like without the permissions), but then saved them on the remote target as well - making them unique there as well.
So now you have added permissions on the development target, which of course doesn't get populated automatically to the remote already saved target. So you have to make the changes there as well manually.
Note this is only because you made target specific changes ones then those changes have to me kept manually in sync.
If you want just to have a single set of settings then make sure you change the settings only in development and not on each target again.
The overwritten settings are saved in:
./wappler/targets/_target_name_/app/modules/SecurityProvider/_name_.json
if just remove the files from the targets that you don't want to overwrite manually any more so that they will receive the default development settings.
This kind of issues will be definitely solved with the new targets manager where you will have clear overview of all targets and their settings. We might even allow some partial overwrites per target.