As far as I know, Fidelity generates a separate Form 1099-R for each account from which distributions are made on which it shows the total of the distributions made just from that account during the year. Even if Fidelity did combine distributions from separate accounts onto a single Form 1099-R, the transaction records that Fidelity provides would show the separate distributions from each account.
Whether or not a distribution is an RMD seems to have no bearing on whether or not the distribution is exempt from Hawaii tax. What seems to matter is the nature of the account from which the distribution is made.
I can only guess as to how accounts containing comingled funds would be treated. The instructions for Form N-11 and Hawaii TIR 96-5 appear to indicate that Hawaii considers as exempt from tax only distributions from retirement accounts that contain funds attributable entirely to amounts funded by employer contributions and not by employee contributions, so I would guess that distributions from IRAs (including SEP IRAs) that contain funds derived from employee or individual contributions would not be excludible.
