dos2unix doesn't convert ^M

I know you have gotten this resolved, but I wanted to add a note for reference, based on some testing I've done.

If less is showing ^M, then like Sybren I suspect it is a MAC style ending (\r), not DOS (\r\n). You can determine that easily using cat:

$ cat -e filename

• Unix endings (\n) show as $
• MAC endings (\r) show as ^M (less shows these)
• DOS\Windows endings (\r\n) show as ^M$ (less does not appear to show these)

Use dos2unix to get rid of the DOS (^M$) endings

Use mac2unix to get rid of the MAC (^M) endings - dos2unix won't get rid of these.

I had a file where I had to use dos2unix and mac2unix to get rid of all the non-Unix endings.

\r denotes a carriage return, and on MAC it is used without \n to denote a line break. Are you sure the file is in DOS (\r\n) format and not MAC (\r)?

If VIM really turns out to be the only thing that'll repair your files, you can also invoke it as:

vim somefile.txt +"%s/\r/\r/g" +wq

This will open the file, perform the operation, save it, then quit.

Can you give us an example of the file, so that we can investigate further?