With a used balancer there is always a chance that it was rebalanced to another assembly and won't work right with your engine.
If you knew specifically the engine that it came off of and it was never touched new from Ford, then that's a different story but how can you be sure now?
Since your engine is running fine, personally I'd keep the degreed on the engine and the one you just bought on the shelf. When it's time to sell it offer it to the new buyer.
Keen eyes will notice it on your car and will suspect a S-A blueprinted race engine in it. Why disappoint them?
There are all kinds of day 2 cars. Many are just a bit better then as delivered.