The cache depends on a few global GO settings. Deleting "GrandOrgueConfig" reverts them to the defaults. If you had used different settings, the cache can be invalidated.
If you have not saved yet ("Revert to defaults" not available), you can use Reload instead of "Revert to defaults".
GO has no expectation, how the MIDI setup looks like. If the devices are connected via different MIDI ports/interfaces, they may even use the same channel.
Many users have troubles with understanding the intial MIDI config, therefore we consider it as function for advanced users and it is disabled by default. Normal users just should right-click on the manuals, stops, ... and save.
The logic behind the initial MIDI config is:
* During loading, If there are saved settings, load them as current settings.
* During loading, If there are no saved settings, COPY the intial MIDI settings for the various elements as current settings.
* Right click on a element changes the current settings.
* Save saves the current settings
* Revert to defaults deletes the saved settings and reloads.
So initial MIDI only affects the organ during loading. The order of the manuals is defined in the ODF (eg. what is manual 1).
Your posts mostly looks like, you have troubles understanding the initial MIDI. So my first recommendation would be to avoid using it. If you want to use it, please try to understand the simple rules from above - if you still have a case, where you don't understand, why GO behaves that way, please ask specific questions.