Greetings,

In regards to the specific point about losing Desynthesis skill, the system is indeed working as intended. When you are skilling up a specific craft another craft's skill may randomly lose Desynthesis skill points.

Here is a direct quote from the patch notes: (I see that Maluber also posted this information, but lets make it official.)
Successfully desynthesizing an item will raise your skill level for that class. However, this may also lower the skill level of other classes in certain instances.
* If the skill level increase would bring your combined skill level over the 300 point maximum, the skill level of other classes will be lowered.
Good luck to everyone desynthesizing, I know I need it! :P