I reported this problem of losing breakpoints and bookmarks in R4.5 a while back and it's still happening in R#5.The reply from Jetbrains was something like "It's working fine".
Here's a simple test case. (done in R#5 build 1570, the latest as of today, VS 2008 SP1)
1- Add a bookmark or breakpoint on some code line.
2- Insert 3 (or any #) blank lines just above the line from 1.
3- Do a reformat code.
1- It deletes one blank line instead of all 3. What's the criteria for deleting blank lines?
2- The breakpoint or bookmark is gone. I expect the bookmark or breakpoint to move along with its line to the new location.