Electronic Voltage Regulator Upgrade

The same 2 wires ( a blue and a green ) will route to the regulator and alternator regardless where those components are located. My preference is "high and dry" locations for electronics. Not that I plan to go splashing through large puddles, just retaining the ability to.
So
1. What do I do with the old wire ends from the original vr location if I relocate near the alternator and
2. Should I remove the alternator jumper wire and discard it from when I upgraded to the square back unit.
Thanks