To only change the metadata, use the
Java Mobi Metadata Editor. There, remove the old CDE type header if set and put a new CDE type header EBOK in there. I have not specifically tested this, but I was able to successfully remove various headers from multiple mobis so far. The only caveat: Once I had edited a file's headers, subsequent header edits of that edited file broke the file, so better keep the original, just in case.
BTW,
here is a known header list for reference.
This will allow syncing without uploading it to Amazon (where they strip the EBOK CDE type header anyway).