The _Clip hooks are actually responsible for ground collisions. They must start from _Clip00 and next one must always have the next number, if you skip one number all the rest with bigger number won't work. If you have two with the same name, then one of them won't work. For example, if you comment out _Clip hooks of a wingtip mesh, then that wingtip will go into ground or water without colliding, and all other parts with bigger _Clip numbers will go into ground too. Once there was a version of Me-262 with _Clip00-03 removed from prop meshes, and the result was that plane loaded and flew OK but managed to fly under ground and though mountains without any damage as long as altitude was non-negative.
You should just place _Clip00-03 to edges of propellor (_Clip00-01 to Prop1 and _Clip02-02 to Prop2 in a twin engine plane), see this A6M prop as example:
[Hooks]
_Clip00 <BASE>
_Clip01 <BASE>
_Clip02 <BASE>
_Clip03 <BASE>
[HookLoc]
1 0 0 0 -1 0 0 0 -1 0.009 -0.013 1.512 //tip of first prop blade
1 0 0 0 -1 0 0 0 -1 -1.312 -0.013 -0.749 //tip of second prop blade
1 0 0 0 -1 0 0 0 -1 1.304 -0.013 -0.762 //tip of third prop blade
1 0 0 0 -1 0 0 0 -1 0 0.415 0 //tip of spinner
Then you should place _Clip hooks to every edge of main parts that might collide with ground, like tips of each wing section, tail surface, nose, CF and tail. One good example is that when you nose over in take-off or landing in stock Fiat G.55, your nose will sink into ground since engine has no _Clip hooks. Then you can check my fix with three next _Clip hooks after largest number in stock plane added to tip of engine mesh that stop nose from sinking into ground.