If you set the "Tags sync behavior" to merge in the UI, the procedure you describe should work.
As long as pictures can be matched by the date time at which they were taken, renames of the files should not matter. If you have multiple images that were taken within a second, then matching is more difficult. In that case the title on Flickr should match
the filename (without extension).
The directory structure is not important as long as all pictures you want to sync are in one set on the Flickr side and in one folder or subfolders of that folder locally. Make sure you check the option "Include subfolders" in the tool.
Reading the metadata of all pictures from Flickr is not very fast, so you might want to start with a smaller batch of pictures to verify that the procedure works. Say with a 100 pictures.
Let me know when you encounter any issues. Have fun synchronizing!