this is true for configuration (*.cfg files) related parameters (not for items)
If you remove an item from a flat *.items file, it should be removed also from OH2.
Items coming from flat files are not stored in an another destination (in $OPENHAB_USERDATA or jsonDB or somewhere else) after they have been loaded by OH2 in memory. Same applies for Things in flat files as well.
There is a workaround the stale configs issue: place the config pid as the first line in your *.cfg
This will overwrite any existing stuff in the ConfigAdmin and as a result, clean the output *.config file from old stuff and place only the new parameters coming from the *.cfg file
example for addons.cfg:
pid:org.openhab.addons
package = expert
ui = ...
voice =....
so forth
This workaround for the stale configs applies to all configurations (*.cfg files) that have a config PID… e.g. mqtt, influxdb, mail, etc, etc… mostly stuff in /etc/openhab2/services/
This is because the ConfigAdmin will read both *.cfg and *.config files and load all parameters.
Stuff in *.cfg take precedence but if you remove (not change) a parameter from *.cfg, it does not get removed from the *.config