I don't have a "tried and true" method, but have done a bit of research into it as I'll be facing similar challenges as we grade with Resolve and have just switched to Premiere. Due to codec issues (.mts media that Resolve won't read) I'll be outputting a flattened movie file and using scene detector to cut it up, and then exporting any shots with disolves seperately with handles. NOT ideal I have to say, I think Premiere has some work to do in this area.
In your case though where all the media is readable by Resolve; have you tried using the project manager first to make a trimmed project, and then exporting the xml from there? I think that will give your media unique file names.
I have just finished ( an hour ago) a Resolve and Flame post prod session to finish 8 TVCs .
I edited in CS6 and simply exported an edl and supplied the finishing house with the source footage.
This was conformed into Resolve and then onto Flame (as DPX) for compiling once we finished the grade / cc.
I was also dealing with duplicate filenames as well as... and I manage this by organising the source folders.
Another thing...I dual record source files. One internal is AVCHD. The external recorder is ProresHQ so I edit the AVCHD and finish with the Prores files. This means the filenames are different and need prior organising.. but...
Resolve has the facility to manage this perfectly by way of looking for the timecode instead of the filename.
(maybe your DSLR does not produce timecode so you are going to need to adapt this somehow!)