The previous two answers "but it is better not to draw on this" and "should only be drawn upon in extreme circumstances" express this act of protein catabolism as a deliberate, conscious action. But protein catabolism is not deliberate - it is a pathological mechanism which is triggered when the body is in a state of malnutrition.

Therefore I would recommend rephrasing your text:
"Va anche detto che nell’organismo esiste una sorta di magazzino proteico che è meglio non intaccare: quello dei muscoli. Non a caso quando l’organismo viene lasciato per molte ore senza proteine, le “smonta” nei muscoli stessi, con il rischio di intaccare questa preziosa riserva."

Something along the lines of:
"Skeletal muscle acts as an important protein reserve, and when intake of this nutrient is inadequate, the body draws on these precious stores, leading to muscle wastage."

"If not enough energy is taken in through diet, as in the process of starvation, the body will use protein from the muscle mass to meet its energy needs, leading to muscle wasting over time. If the individual does not consume adequate protein in nutrition, then muscle will also waste as more vital cellular processes (e.g., respiration enzymes, blood cells) recycle muscle protein for their own requirements"
https://en.wikipedia.org/wiki/Protein_(nutrient)