Hi IClampers:
Okay, there's a few concerns here:
1. loaded and unloaded beams.
2. statically loaded and dynamically loaded beams.
You'll need to consider which case(s) you're dealing with.
Bridgebuster is correct to cite the fatigue and stress raiser issue. By his handle, he is involved with bridges, therefore dynamic structures. I've never been very concerned with welding across a flange on a statically loaded structure. I've seen hundreds of spliced beams.
I've always been concerned whenever welding on any loaded structure. Common sense should tell anyone that. Steel does not respond well to stress when it is cherry red.
Evelrod is right: Use jacks or whatever to get the load off the beam, then weld.