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Figure 2.8 shows an example of what the paragraph 2.8.3.5 is talking about...but that shows a plate on the top flange.
I'm not grasping your question completely about how the stiffener plate is welded in the web and to the flange(s)(<---depending whether it was a full depth stiffener or not) I think that I would take a pic of the weld(s) in question and ask the EOR whether or not the welds need to be seperated or left "as-is".
We had some flexible connections welded up completely by a welder who missed the "5/8" return at the top" and welded the clip angles completely across the top.....the EOR said to leave it, this time....so it might be worth the question to the EOR to save the expense of repairing.