The solution was to copy the schematic library symbol to another name. I used the library editor to copy my part definition in PADS to match. Suddenly my net connection worked. I reverted the name change without changing anything about the symbol/part/decal definitions and I still get to keep my net. That's a pretty insidious bug. Clearly, the software previously noticed changes and was able to update parts, silk, etc. but did not push everything. My only clue was a warning when annotating in a particular direction as described above.
If a "duplicate" pin (which I couldn't make intentionally if I tried) can result in the software choosing to make netlist edits it should really be a full stop error, not a warning. The software should not guess the intent of a designer for the same reason compilers don't throw away code. If it knows you're wrong, fine. Stop working and give a useful response. If a compiler generated executables with chunks of libraries thrown out because of a warning level event there would be outrage and brimstone.
Selection filter> [x] Objects - got it. Thanks for the help.