I have had exactly the same problem you describe. Duplicate markers in merged clips and loss of marker data. I spent about an hour speaking to an Adobe customer support representative and after we did a screen share, updated CUDA drivers and all sorts of other, seemingly unrelated hurdle jumping, he told me that markers are not supported within merged clips. This revelation did not come at the onset of our conversation but at the end, just as he was about to escalate the case. My sense is that the marker system is on the half-baked side or, since merged clips were a somewhat recent addition, somehow fundamentally incompatible with merged clips, thus requiring a significant rewrite of the software.
I explained as firmly as I could that using markers within merged clips represents, what I consider, a very typical work flow. The rep tried to explain that I could add markers to clips prior to merging them. I told him this wasn’t sufficient and he then said I was free to post a feature request to the Adobe site.
So, in short and according to Adobe themselves, markers don’t work with merged clips. That leaves me searching for an alternative workflow when editing interviews shot dual system.
iMac Intel Core 2 Duo 2.16 2GB