Blender does not save new transform after mirroring

I would like to mirror a hip joint, i.e. two stl files (an stl file for the femur and another for the pelvis) where objects are close together in a specific position. After I mirror the objects and export them as stl files into another software, the femur is far away from the pelvic bone, which means that the new transform is not saved by Blender. I thought I could join the objects, mirror them as one object, and then separate them, but the software cannot separate them (Space-edit etc). I have also tried to use a new centre from the transform option from the Object menu at the bottom, but in joined objects, it does nothing. What else can I do?

You need to be more specific exactly what you want to do. Screenshots, attach example blend files etc so we can understand what’s in your mind.
Blender certainly can separate previously joined objects pretty easily (in edit mode press P / Separate Loose Parts)

Sorry, I am a beginner in Blender. I have two stl files, one for the femur and one for the pelvis. I import them into Blender and I would like to mirror them and export two stl files as well (one mirrored femur and one mirrored pelvis) but close together, i.e. as a joint. I know how to separate joined objects, but in my case, it just doesn’t work.