You can leave it connected to the battery, just don't let the end that was connected to the B+ terminal contact anything metal and cause a short. Also it looks like the purple charge wire should be directly connected to the positive side of the battery. But there appears to be a 20 amp fuse in that wire. If that fuse(small chance) is blow or corroded(larger chance and possibly melted fuse holder) will cause the issues that you are having with the charging system.
This bypass wire is just replacing the purple wire in the diagram. If you get the temporary wire connected and it then charges then we know that the problem is in the purple wire. And you can go ahead and use your temporary wire as the direct replacement for the purple wire.