Application group errors

[pverar]

I want to cleanup a number of vsys contexts which all have their policy and objects managed from Panorama.
I load the config from my Panorama device in a new project and can edit it without any issue and generate the cleaned xml file.
Although when I load the cleaned xml on Panorama I get a number of errors as following:

device-group -> VS-NAME -> pre-rulebase -> security -> rules -> RULE-NAME -> application 'APP-NAME' is not an allowed keyword

All these seem to be related to custum URL groups which exist on Panorama, when checking in the MT under 'App-ID' I can see these groups are there without any members.

I'm using MT version 3.3.15

Any idea?