This was a trustee to trustee rollover; the money never hit my account. I called the 2nd originating 401k servicer and they said that, because it was a trustee-trustee rollover, it is their discretion whether to issue 1099r's, so they choose not to issue them. Should I just report the one Form 1099-R that I received on my Form 1040 or should I use the Form 5498 to report the entire amount? None of this is subject to tax.
Are you sure that originating and receiving accounts are 401(k) accounts? I suspect not. A trustee-to-trustee transfer of an IRA to another IRA of the same type must not be reported. It is neither a distribution nor a rollover.
A 401(k) and an IRA are two different kinds of accounts. Any account from which you receive a Form 5498 is an IRA, not a 401(k).
With regard to a direct rollover from a 401(k), it's entirely untrue that the reporting of a direct rollover of a distribution from a 401(k) is discretionary. It is required to be reported. From the Instructions for Form 1099-R, page 3, Direct Rollovers: "You must report a direct rollover of an eligible rollover distribution." Since the plan refuses to issue the required reporting, I suggest contacting the IRS as described in Tax Topic 154: https://www.irs.gov/taxtopics/tc154