New SF86 or tie-in to existing investigation?

Hello all,

Company A: Commercial Company that I worked for (never needed clearance).
Company B: Offered me tentative job offer and submitted my clearance. Its been 13 months, investigation is under process. Never joined this company.
Company C: Started with them 5months ago, now they want to submit for my secret clearance.

Company C wants to submit for my clearance, and I had to remind my supervisor that my clearance is still under process by a DoD contractor that I never joined. My supervisor called our internal FSO and they said if thats the case, they would just have to add a note in the JPAS stating that Company C is also interested in this candidates clearance. Speaking to internal FSO it sounded like I dont need to re-submit my sf-86? Has anyone heard or gone through similar situation. My concern is I want to take less risk and dont want to ruin my chances and having to wait another 13months while I may be close to get the full clearance. If Company B still keeps sponsoring than do I need to add more complexity to my case by having company C add to my clearance? What shall I do?