I had a series of errors recently while I was trying to run a few geoprocessing tools manually on layers within a group layer. The error message kept saying it couldn’t open the layer, even though the layer was clearly in the map. Even restarting ArcMap did not help.
I eventually discovered that geoprocessing tools may randomly fail on layers which are part of a group layer. I say randomly because sometimes the tools would run as expected, other times not. I’ve only experienced this anomaly when using the ArcMap interface – running the same sequence of tools on all the layers in a group layer in a for loop in Python does not give this error.