I don't think EDTA will damage the column, but I also would be surprised if it helped clean it. Try high salt (1M NaCl) and low pH (pH 2) washes, also.

I am not sure how it works with EDTA,..

but we use Sephadex columns in our lab.

And cleaning process we use is:

overnight shaking incubation of column(with clean buffer) at higher temperature than optimal temperature of protein [say 50-60 degrees for proteins stable @ room temperature],.. after that the buffer is drained and fresh clean buffer is run through column

You can use 2% EDTA for cleanliness, or use hot water treatment of packing material, the best way to clean the matrix is take it out suspend in PBS buffer, centrifuge at 5000 rpm three times and repack it.

thank all of you

Adam: for Amersham nickle column stripping, they have a protocol that used EDTA as cleaning agent.