Your other option then is to take your 29.97 rushes and convert them to full quality 25 fps rushes. These then become the clips you link back to at the end, and the clip you use to make your proxys with. If necessary, you could go old school, and create a pull list, after the edit, and retransfer the shots you need for the final edit only, recutting the shots in.
As Shane posted, you really are doing this incorrectly, and although the work around is working for now, at some point, which you are now basically hitting, things will start to fall off the track. If your offline and online programs aren’t using the same timecode, you are asking for trouble. Timecode is pretty much the most important aspect of these types of workflows.
Glenn