I would suggest the  proper place to pose this question is with the agency where you hope to work...that said changing jobs shouldn't delay the background process ..but your new employer might be a little miffed when contacted by the background investigator..particularly if the spend money to recruit you

I recently was offered a COE for an intelligence agency and I just turned in my completed SF-86.  I have nothing to worry about in terms of the clearance going through.  I am currently employed in the private sector but I am very unhappy at my current job.  I was offered another job in the private sector for a different contractor doing work I actually enjoy.  I was wondering if I were to accept this new job in the meantime while I am waiting for my TS/SCI to be completed and then leave about a year later to work for the feds...would this disrupt the clearance process in any way or possibly hurt my chances at all (besides hurting my resume just a little).  Also would I have to contact OPM and update my employment info.?
   I am just worried that there may be some glitch somewhere along the way and I may mysteriously lose my COE and I would rather be at this new company instead of my current one if that were to happen.