If you mean the 'C' section braces up in the top centre of the rear fenders,a lot of guys with radically lowered trucks seem to do this often,and I haven't heard of any real problems.
AFAIK it's an easy thing to do,leaving just two small holes to fill.
Chevrolet obviously considered them necessary but I assume your truck will not be used in a commercial sense,i.e lugging heavy loads around any more....
I imagine you'll be OK.
