Replace clips in PPro? WONT WORK

So, I had a nicely edited sequence in Premiere. However, I needed to edit all of the clips that were used in the sequence (literally, the files of the clips) in AE. Then I rendered and exported those updated clips from AE into a new folder. Once that was done, I deleted the folder that contained the files that the PPro sequnce was using. When it asked me "Where is file x?", I located it and it imported the rest of the files perfectly since I named the files to have identical names to the older files. Now, most of the clips updated correctly. But there are a couple that have lines through them (clips) that are extrememely difficult to replace. Am I doing something wrong here?
Thanks

Try cleaning the media cache database and let the indexing, conforming and creation of peak files finish before editing.

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