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After clipping a reference file the snaps and flood commands still recognize the elements within the reference but outside the clip boundary.
I agree with Bob Rayner that this operation is possibly a defect or could be an operational issue. I any case it is not something that would require an Enhancement which is why you would post to the "Ideas" forum. If this is a continuing issue for you then you should post it to the MicroStation Forum and maybe provide an example file.
Yes, this one kind of feels like a bug.
Connect Edition update No. 9. We also ran into this issue in V8i.
Which version are you using? I had this issue up until Connect Edition Update 5, then it was fixed with Connect Edition 6.