We\'ve had this happen more than a few times were we consider it to be more than a fluke at this point. When we are merging back after we are complete with our branch there
The comment above with the "No to all" option in the undo confirmation dialog works okay, but as commented by Mark Hosang, this will not work right if you have new files. Mladen Mihajlovic is right that you can make sure to not select those new files. However with a large code base, wading through this is very tedious.
So my method: before getting to the confirmation dialog, you are presented with a window to select which files to undo. This window has sortable columns. You can sort by the Change column and select only the files with merge status (these are the unchanged files; merge, edit are edited files and merge, branch are new files). Just click Undo Changes with just those selected, and then enjoy the beauty of an uncluttered merge changeset.