I have worked around this issue by moving the edited audio files into a new folder on my PC and overwriting them in the project

EDIT: I spoke way too soon! When importing the new files from a different folder, their durations in PD show as around double their actual duration (It may be old duration + new but I haven't tested it). This has made it even worse.

Even when opening one of these files in a completely new PD project, it displays the duration as double - Is there a way to clear where PD stores what it thinks the audio file is or something?

There are sometimes problems like this with "ghost" clips that PD has cached away somewhere. This is common if you had used the Render Preview feature for this project. You can try manually deleting the temporary files from the Preferences menu, although you may have to close the current project so that the files aren't in use.

You should verify the length of your original and edited sound clips using MediaInfo, or uploading sample clips here for others to inspect.

Normally, deleting or renaming the original clips and browsing for the replacements when PD can't find them is a solid approach, but you can run into problems if new clips aren't as long as the duration of the previous versions were on the timeline. In that case, it's probably quicker to just start all over and delete the original project.