How did you conform your proxies? If you conformed using “Interpret Footage” within Premiere, it only changes how premiere handles it without actually altering the original file, so the file is only slowed to 25fps within that project. When you relink the media, there’s an option to “Preserve Interpret Footage Settings” that should “re-conform” the clips you’re linking to.
If, however, you conformed outside of Premiere, then your proxy files have actually been slowed to 25fps, and premiere is seeing them as 25fps files rather than 50fps that you’re telling to interpret as 25. In this case, you’ll have to use the same external conforming process you used while making the proxies with your original files.
Now I’ve got a question for you…when you relinked your files, was there a way to relink everything at once? I’m working on a project with SD .avi proxies, and when I try to re-link to the h264 .mov masters, only the first file I actually try to relink does so successfully. The rest automatically link back to their SD versions, forcing me to have to relink the files one at a time.