Should I be worried if my Secret security clearance as an Army Chaplain Candidate has gone wrong due to having an SF86 done on my behalf?

Relax. As long as you fill out the new SF86 to its entirety and to the best of your recollection, and can fill in those blank spots/clarify the discrepancies, then you should be fine. If your recruiter did fill in your blanks, you may want to have a talk with them. Ask them if they actually did try that. They may have been trying to do you a solid....but should have just let you do it.

Wait - an SF86 "done on your behalf?" In all my years as a security manager, I have never heard of an SF86 being done "on someone's behalf." I'm not even sure how your recruiter filled out and submitted a SF86 in your name. I could see how maybe that was done prior to eQIP with EPSQ.

I mean I didn't realize what I was filling out with my recruiter but now, in hindsight, realize it was basically the SF86. Then at reception they went over my SF86 with me because I remember thinking "Man I'd hate to do this as my job." (And then ended up in BN, BDE S2 and doing security manager again). But they definitely went over it in reception before basic. Then I had my interview in AIT and this was even for TS.

But with the recruiter I filled out everything - and for TS it was 10 years or 16th birthday whichever came first (which at the time was 16th birthday came first). The recruiter filled out nothing on that.

This: "I had to fill out basic information through a link they provided which asked for the last 7 years of my life." That sounds exactly like the SF86 for a Secret that you filled out in eQIP. There's no other reason you'd go back 7 years and it's all done through eQIP now. You did do an SF86 - unless your recruiter was cc'ed on the email to log in they couldn't have changed things. Although I feel like them logging into your eQIP would be wrong. I'm not sure. I've never gone and logged into someone's eQIP even though I get cc'ed on all the PSIP requests I send in when they are approved and sent an eQIP invite.

Is this your initial investigation for a Secret (as in your first time having a secret through DoD as a servicemember)?

If you explain to the investigator what you think happened, they probably won't deny anything. They look at a whole person standard with clearances. You shouldn't have anything to worry about but I've never heard of anything like this at all as long as you can show why the info was missing.

When I first came in and was in BN S2, we made people do a hard copy SF86 before we had them do it on EPSQ (and then eQIP). And yes, people do fuck it up a lot. I even made an Idiot's Guide to the SF86 and people still messed it up. Which is why we had them fill out a hard copy first.

This is why you meet with an investigator. To fix the gaps and fill in anything missing. The gaps most likely represent what happened after you left the service. Not a big deal and easy to annotate and fix. Nothing to get emotional or upset about as long as you fix what the investigators identify and respond promptly. Just keep working with the investigator. You'll be fine.