So, I took a little break from this and came back yesterday and managed to figure out the work around. Thank you PoP for the recommendation, I was able to use Java Mobi Metadata Editor to solve the syncing issue, however I have ran into another issue with the splitting process. It seems I'm destined to fail.
After splitting the file into it's .mobi and .azw3 parts, which is required for the mobi metadata editor. The layout of the files changes, as seen here
https://imgur.com/a/KoXJfqE. The split file also now includes multiple blank pages. As you can see, I've tried it with the example file as well, with the same results. I've tried to find any mention of this and have been unsuccessful, so I'm not sure if I'm doing something wrong or not. I'm using the Calibre Plugin for Kindle Unpack. I've also compared the metadata for the pre split and post split files with no differences noted after the split has initially occurred.
Any help would be much appreciated.