Question-do you have a lot of edits that share the same source files (take)? One issue may be that in the case of a handles sequence that you may be creating a lot of trimmed R3D files that have same meta data and overlapping timecode, which would naturally create conflicts when the trimmed files are added in to media pool.
I sometimes conform the R3D files with XML and carry across repos. Then dial R3D settings and render out the tied sequence DPX frames at target resolution and use edl with the newly created preconform DPX sequence. Any changes can go to a top layer and you can use proxies if needed.