It is absolutely safe!
I have a different view of their use though.
If you are using Goex 2F or 3F, or any other Real Black Powder, not a substitute like pyrodex or whatever, you do not need magnum percussion caps. Remember real black is lit off by the sparks of a flintlock so as long as the flash channel is clear, clean and dry, and the powder is dry, they are just not needed with the real stuff.