Take photographs of the wires where they connect to your alternator, and put labels on each wire so that you have a record and proof of where each wire should connect.
When moving the engine to enable access for replacing the gaitor, it is necessary to disconnect the wiring from the alternator, and the guys who worked on my MD2020D put those wires back to the wrong alternator terminals. I was not present when that work was done on my boat, but running the engine later when I was able to visit I noticed that the tachometer was not indicating. A quick check around revealed some of the wires were connected to the wrong alternator terminals so I called the yard manager and a technician came and sorted things there and then. I was fortunate having spotted the problem, and the engine was stopped immediately. I don’t think any serious damage occurred, and the engine and alternator have run properly ever since the job was done about eight years ago.