Fill out SF86, again?

I am in the process of doing an inter-company transfer. The FSO representing the office I will be moving to asked for my clearance info and was able to find it pretty easily on JPAS. I currently hold a DoD TS/SCI that I was approved for less than a year ago. The FSO however told me that my current DoD TS/SCI is not going to transfer with this customer. He explained that while the contracts they work for are also at the TS/SCI level, I would have to fill out my SF86 all over again since it is a different customer. Last time I filed out the SF86, it was on eQIP which was pretty easy, but now I am asked to fill it out as a fill-in PDF, which in and of itself seems a little strange.

Correct me if I am wrong but aren’t there only two “types” of clearances? You’ve got the DoD ones that are Confidential, Secret, TS, etc. and then you have the DoE ones that are L and Q.
If I am going to work at the same company, working at the same clearance level, and to top it all off my clearance is relatively new (<5 years), Why am I being asked to fill out the same SF86 that I filled out a 2 years ago? Is there any transferability with my current TS/SCI? He couldn’t disclose who the customer is, but he did say my DoD clearance will not work. So if its not a branch of the military, then that really narrows things down.

Can anyone make sense of this or that has been in a similar situation? I really appreciate it

You are being asked to fill out a new SF86 (on paper) because the new agency does their own investigations/adjudications. Welcome to the harsh world of non-reciprocity.

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