The gain calculation only applies to the return of contribution from the traditional IRA. The amount to roll over late to the Roth IRA is the exact amount distributed from the designated Roth account in the employer plan, regardless of the adjusted amount distributed from the traditional IRA. Treat the return of contribution from the traditional IRA and the completion of the rollover from the designated Roth account in the employer plan as entirely independent transactions. In fact, if you had a source of funds to do so, the completion of the rollover of the distribution from the designated Roth account can occur before the return of contribution from the traditional IRA.
