Here's what I think you want to do.
1. You have three hundred and forty-five separate .dgn files.
2. All three hundred and forty-five are attached to a single reference file.
3. You want to detach them all.
EASY WAY: rename, move or delete the reference file. The 345 files won't be able to locate the reference file and thus it won't show up. This will have no bearing on the files in-question other than the reference file's info no showing up. You won't have to do a thing to the 345 files.
HARD WAY: File-by-file. I don't know of a batch process that wouldn't involve a lot of self-abuse, so I wouldn't even touch it.