I recently sprayed over some black sharpie with some Rust-oleum ultra cover That was Matte Clear.
I didn't notice any effect to the sharpie. I sprayed two coats on. About a hr. apart. Temperature was in the 50's and the first coat was completely dry.
I sprayed Fluorescent Yellow Krylon for My Cap Dip color and just used the black sharpie to touch up the end of the Cap. It did melt into the masking tape a little. I waited til the next day to remove the tape and it was fine.
Hope this helps.
bretto