and if you generate QC instead that ruins your model's animation data?
No. Open your model and then you must generate a new qc file with your model's name, this way the qc file will include the path for all its textures, then copy-paste all the animation lines, don't use the origin and textures of the model of which you took the skeleton.
If you assign the vertexes of your model to the right bone, once you compile it it will perform all the animations as if they were done for it. The process is like this.
1.Import reference.smd of the decompiled HL model. Delete all faces and vertex.
2.Import your reference.smd, it only need a single bone. Once imported, delete that bone if you import the mesh along with the bone.
3.Assign vertex and test when finished. Use another copy of the original HL model and check where its vertexes are assigned in case of doubt. Now it is time to generate the qc file.
4.Once done export your reference model into the very folder from where you took the HL's reference smd, replace it if necessary, but warning!! it sometimes has another name, like your "ZOM_template_Biped1", if so change the name into the qc file.
5.Compile normally. It must work.
6.If textures are misaligned, use the texture alignment tool inside milkshape.
If all that does not work, well... Oh, c'mon!, It must work!!