No matter where the device is used if you go against the OEMs instructions during a repair or modification on any medical device, the liability lies with YOU! That being said if the company don’t specifically tell you that you can’t use non OEM parts in the service manual then use whatever will do the job.
CE marking just means the device has conformed to the relevant EU directive for its stated purpose, which also means if you use a device out with its original scope it is also not CE marked and hence the company will not be held responsible for any resulting altercations.
To modify medical devices it would be prudent to have ISO13485:2003 registration (along with the standard ISO9001)