First, thanks for trying my utility. Now to address why things don't work as well as I think they should.
In the Readme it details that the data file is made in each folder. The trick is to copy the folder as a unit or make a TreePad file from the comments to date, then delete the comment file. Possibly importing the generated TreePad file into some system-wide TreePad data file if that's what you want.
In the old incarnation, CommentConfig, I had 2 more shell extensions that you could use to copy or move the file to another folder via context menu or drag & drop. The destination key would be added to the central data file and the comment copied. The comment would seem to move with the file. A weakness of this system is that you have one central data file. Every time you hover the mouse to get the tooltip, it loads the entire data file. If you do a lot of comments, that's some bogging down of the shell(which isn't all that stable to begin with.) Also you fall into the trap of drive letter reassignment. If you try to copy across a network or make another partition that changes the drive letter assignment, or move your commented files to another machine altogether, stuff breaks. And, since Windows file paths are not case sensitive, Windows isn't very picky about getting it right(do a search on an existing folder named MyFolder using the string myfolder and chances are stuff will come up named "myfolder" so now if you have the entire file path as the key you need to do case conversion on every entry during the search, slowing things down even more.) That's why I say ideally the FS should handle it.
One of the reasons I put the button to convert to TreePad format was as an escape from this dilemma. You can convert to TreePad and break the dependence on the key/search mechanism. The Tooltip should really be used as a stopgap convenience. Or if you prefer the Tooltip mechanism, do one to one folder backup. Merging, even if you concatenated the comment data files, would end up with something overwritten. If all files of the same name had identical comments then it wouldn't matter. As the Tooltip search is going on all the entries in the local data file are sucked into a Map that doesn't allow duplicates, as a filter to avoid repeat entries. But if MyFile has one comment in one folder and a different comment in another.. well you see what I mean.
After messing with this since 2001 I came to the conclusion it's much cleaner to have a data file in each folder. Trying to monitor file operations to intercept stuff would slow things down too much. I don't think there's a practical way to implement merging or moving files and carrying the comment. The FS is really the only thing that should have the ability to store annotations as part of the file. The alternative would be just to make a database like with your DVD collection.
After a long time of messing with this I'm sorry to say I don't think there's really a good way to do it in Windows. Maybe if I had VMS file system to work with I could use some RMS or other mechanism that's available to write something smooth. As it is, the utility is a hack. But within its limitations I hope it may be a hack that's fun to use for the small convenience it can provide.