Is there any way of combining the HTML files so they merge?
HTML is an open standard. The bookmark files are open-source.
A few minutes with the built-in Linux / Unix / BSD weapon of your choice (awk,sed, perl etc. maybe with a bit of diff and rsync for good measure.) and Robert is your uncle.
Can probably do it with Powershell too, but likely to be more hassle (and more lines of code) than its worth.