In a nutshell, yeah.
However, try not to scrape the old sealant off. Or if you do, be very careful not to damage the sealing surface.
Instead, try locating some gasket sealer remover.
I can't remember where I saw it, but I made a mental note to give that a shot the next time I had a cover off.
And when you go re-install the cover, only use a thin coat of sealer.
Too much can be as bad as too little.
Yamabond (of course at the Yamaha dealer) is pretty good sealer.