If im on blood thinners for a pulmonary embolism and currently diagnosed with lupus what difficulties should i expect later down the line medically?

It depends: It depends on whether you have a problems with increased clotting of blood that it frequently associated with lupus. The presence of a hypercoaguable state demands long term use of anticoagulant meds.

Hopefully no issues: If continued on blood thinners will hopefully have no more pulmonary emboli. Can have other organ involvement by lupus which is hopefully being monitored by your doctors.