As has been previously answered, %7E
is the URL encoding of the ~
symbol.
We have had a similar problem when copy-pasting links in the rich text editor. Broadly speaking, what seems to be happening is that when copying the HTML output of the rich text editor we are already working in a browser, which is rendering the HTML source. Links, for example, are being resolved by the browser (so that if an author is logged into Sitecore to edit for one particular host domain but works on a different host domain the links resolve to the domain they are logged in for).
We have had the specific %7E
replacing ~
problem when doing this as well.
You don't quite give enough details for me to be sure this is what is happening in your case, but it seems fairly likely. If you're copy-pasting browser rendered HTML then you aren't accessing the raw strings.
EDIT: This is probably related to a known Sitecore bug with adding path information for the rich text editor to a link when copy pasting. Sitecore have a fix for it here:
http://sdn.sitecore.net/Products/Sitecore%20V5/Sitecore%20CMS%206/ReleaseNotes/KnownIssues%20Recommended/Copying%20and%20pasting%20link%20in%20rt%20fields%20may%20break%20the%20link.aspx