It is apparent that the underlying IX is needed for all the functions of the e-boat, which is a skin placed on top of the IX. By removing the IX you essentially broke the mod, lost all control of any functions needed to make it work. The IX was most likely a quick expedient to get a schnelboat up and working as opposed to creation of a new ship model.
There may be ways to improve the frame rate, if it can be done, by moddding the underlying IX for improvement. Not sure of your modding skills.
Good luck.
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