puh - where I should start here
at first let me tell u that u r totally thinking the wrong way here IMO - free ur mind now!
I dont know exactly what u mean with "lowered the prefab" , but here are some tipps:
If u want to built a prefab that has underground-parts the most bottom-layer of the prefab is also the most bottom-Layer (0) in the prefab-editor (no matter if Pilles or Ingame!) !!! (everything that is beneth the worlds 0 level is falling down - even in editor !)
(Dont care on which hight it must be placed to fit with the surface-Layer of the world when it is spawning in game - this is another topic
and has nothing to do with building the prefab (this has something to do yoffset in rwg or a substraction of the y-value in Navezgane) )
Most important part:
avoid Air beneth the prefab - it will cause it to collapse !!!
Also important when spawning:
In the prefabs-xml the line: CopyAirblocks the value should set to "True" !!!
(if it is on "False" all the air that is supposed to be underground turns into dirtblocks then and u have to dig ur way through XD !)
for example check "xcostum_burialshrine(by_snake0567)" from COMPOPACK
and study how it looks when loaded in the prefab-editor and how its behaive when u click on gametest
Also pls study and compare the prefabs own xml with yours (have a look on the line yoffset !)
ok - i hope this helped a bit
edit:
if u dont have COMPOPACK - "bombshelter_md_01" has also a 12 blocks deep underground-part