From past experience (I'll assume that it still does it) ... when you Import from HTML it will just add that new set of bookmarks into you current bookmarks... thus ending up with basically two sections in your system (in the Places.sqlite file) ... then you would have to manually arrange them to your liking.... but it won't take as long as one would think. As for dups... maybe this?
Bookmark Deduplicator :: Add-ons for FirefoxBut what I would do before you start messing with your Firefox profiles is create a new profile to play with ... it will start out with a pretty much empty file... just remove the bookmarks that get create with a new profile... then import those two files into it to see what you get... and maybe install that extension. Once that is complete... then you can decide on how to handle your main profile stuff... know what I mean?
Two things... back up the profile that you are importing into... always safe to do that...
Profile backup - MozillaZine Knowledge BaseTo create a work profile... the one to test with...
Creating a new Firefox profile on Windows - MozillaZine Knowledge BaseAnd,....
DON'T TOUCH THAT "Choose Folder..." BUTTON! ... unless you fully know all about it.
...and if you need to run that profile at the same time as your main one...
Opening a new instance of your Mozilla application with another profile - MozillaZine Knowledge Base