I've tried that and unfortunately had myriad problems with Vegas on that and other issues. For instance, it dies at 2% when writing an "=" MVC file (1080p24). It also doesn't address the 6 frame (or so) skip at the seam.
Editorially, I've had much better luck using the recently released demo version of Edius3D. Amongst other things, it reliably renders out a frame-packed 3D-H264 file in around 2-3x the program length (as opposed to Vegas' 14x!).
The issue with re-combining these files is a real one though and Panasonic must give us a tool to deal with it. Obviously Sony recognized it for their cameras and PMB has that functionality built in. I would be more worried if their program (HD Writer) didn't "preview" the join properly so somewhere the data exists.