Shortcoming in The Way DOpus Matches Photos on Flickr

This topic was a continuation of "Flickr Error 96" here, but, it's diverged from the original topic so I've started a new one here.

I had noticed that DOpus was not able to match many of my local photos with those on Flickr and I was having to do it manually. As my photos were not in the default location it occurred to me that DOpus must be searching my PC for any photos that matched filename/title or date taken and therein lay the problem. Let me explain.

To keep things tidy I created a partition dedicated to images, J:\My Pictures. In that location I have a folder containing sub-folders for images that I download from my camera located at J:\My Pictures\Fuji FinePix Downloads. Also on that partition I have another folder containing sub-folder where I save my photos once processed and enhanced located at J:\My Pictures\My Camera\ from which I will then normally upload from to Flickr. In both locations the sub folders have identical names, e.g. "J:\My Pictures\Fuji FinePix Downloads\2003_0822_turkey" and " J:\My Pictures\My Camera\2003_0822_turkey", within the sub-folders the files saved in sub folders of My Camera have identical filenames to files in sub folders of Fuji Finepix Downloads. Nice and neat and practical except for DOpus matching them with those on Flickr.

So what seems to be happening is that during the download sequence DOpus scans my PC to see if it can match the photos on Flickr and sees what seems to be identical photos with identical filename and date taken in two locations and gets confused so doesn't match them although it seems to match some leaving me to manually match the greater number, sometimes almost all. What is worse is that after I looked at the properties of photos in some of the username folders I find that quite a few that DOpus initially silently matched were matched wrongly, instead of matching to ones in the sub-folders of My Camera it matched them to ones in sub-folders of Fuji FinePix Downloads and vice versa.

The initial concept of Flickr synchronisation is fine, but, it seems it would work best for someone new to keeping photos on their PC and new to Flickr. For someone with large collections filed logically using duplicate filenames and folders in different locations so that original files and enhancements are both preserved (you never overwrite originals) there arises this problem.

So is there a way to overcome this without me radically reorganising the structure of my image partition? Ideally I would like to point DOpus to the folder I know the Set on Flickr comes from, but, DOpus does a silent scan before I can get to the Search button. Attempting to synchronise all Sets and Pools at the same time seems completely out of the question. I can't see that pointing the default folder in Preferences to J:\My Pictures\ would help either and as I'd often want to sync within both the "My Camera" and "Fuji FinePix Downloads" folders pointing the default folder to either of them could also cause possible problems. If I could edit the path of the wrongly matched photos in the username folders it would be something, but, there doesn't seem to be a way to do that as far as I can see.

Any suggestions?