You are going to need:
1. Total Commander
(or anything else that allows you to rename massive numbers of files)
Probably the best file manager in the world (especially when it comes to handle uploads etc.), it’s not free but the trial version should do the job. Just select all these images (they could be anywhere within Total Commander and choose “Multi-Rename tool (CTRL+M)” from “File” Menu.
In “Search for” field type: %20 then change it to anything you like within “Replace with” field (I guess the best choice would be: _).
Get Total Commander from: http://www.ghisler.com/
2. A simple SQL command.
UPDATE wp_posts SET post_content = replace(post_content,”%20″,”_”);
It just “scans” every post for %20 and then simply replaces it with _
I hope it helps.
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