I've had this problem all day, and it's happened before, too. I am running desktop 10.3.1 and want to produce a very simple buffer from a single parcel. The output is assigned to the same .gdb that the buffer output is assigned to. When I run the buffer, every other feature class in the map from that .gdb breaks the data link and I end up with a map full of red exclamation points, except for the most recent layer. Occasionally this happens even when all I am doing is exported selected features into their own layer. Has anybody else experienced this?
I suspect that the default location into which outputs of your geoprocessing tools are written, has been reset by the upgrade.
Next time you run a tool pay careful attention to the workspace into which the output is being written, and check that against the source of any layer that you are expecting it to overwrite.