You could program a macro to do it in Emacs without too much trouble - if you're used to emacs/elisp, or if you probably could do it without elisp using a Keyboard Macro in emacs, then using ^u^u^u^u^u^x^e (repeat keyboard macro (^x^e) 1024 times; each ^u increases the count by 4x). The macro would be a simple repetition of the commands needed to resolve one conflict in the file. You could also load up all the files with conflicts into buffers, then use elisp or maybe a keyboard macro to resolve conflicts then switch to the next buffer, and repeat that.
I wouldn't be surprised if there's an easier way, but this would work. And even if you have to load up all the files into buffers and then run the keyboard macro, you cando that and be done in a relatively short time.
Pseudo-emacs:
cvs status | grep conflict >/tmp/foo;
load /tmp/foo into an emacs buffer
edit buffer to remove all but the file/pathnames (use keyboard macros!)
load them all into buffers:
^x^( (start-macro)
^@^e (mark (or control-space), then end-of-line)
ESC-w (copy)
^n^a (next-line, beginning of line (set up for next iteration))
^x^f (load-file)
^y (yank saved)
<RETURN> (load it - you could resolve conflicts right here and save)
^xb (switch to buffer)
foo<RETURN> (go back to foo)
^x^) (end macro)
^x^e (repeat macro once) or
^u^u^u^u^u^x^e (repeat macro 1024 times or until BEEP)
Now you have all the hundreds of files in emacs buffers, and you can set up a macro to grab the next buffer, resolve conflicts, and save it - then repeat that macro N times.