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.
Just report the one you received. They are correct in what they told you. The 5498 is informational only, it's not something you enter into your tax return.
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