Hi
how to change waypoint from the manual tilde ~ don´t work????(flaming cliffs 1.12)

It could be that you're in the wrong mode or possibly that the mission has no waypoints. In route mode (US or Russian planes) any waypoints should cycle when you use that key. (unless you changed it's assignment- either on your own or by downloading a mod)

The Russian planes- in Return mode- the key will cycle through the airports. I don't think it does anything in the US planes. The US planes have a return mode of sorts- but it's incomplete, wrong, or both. The mission builder needs to place an extra regular waypoint in the approach area of the desired home plate in order for return mode to be much help. The russian planes automatically set up a nice & neat 15km initial approach leg regardless if the mission maker set up your landing, or if you manually cycle it to another.

Example- many online servers with SU33's have a land base for a home plate. Personally- I will ALWAYS divert to land on the carrier unless it is located WAY (150km+) out of the way.

It might be that the assignment in the OPTIONS has been changed (as Konkussion said).

Or it might be that for your countries keyboard layout it is a different key. This has caught me out before with other things. My UK keyboard is a little different layout to a US keyboard, some keys are in different places.
For me the key to change waypoints is the key with \ (and |) on it.
If I press the key with # (and ~) on it, I go to the radio commands.

If you can't find which key it is by experimenting, then you could change the assignment in the OPTIONS yourself to force it to be what you want.