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For Cycle 3, the IRS required that the plan document explicitly specify the determination period for calculating matching contributions, including safe harbor match. Take a look at item C.18 in the adoption agreement. If the adoption agreement says the determination period is annual, and the employer calculates and deposits the match each pay period, then a true-up will be required. If the adoption agreement says the determination period is per pay period, then a true up would not be allowed unless the plan were amended, and then the rules for mid-year changes to safe harbor plans would come into play. If memory serves me right, FT had a FAQ sheet about this back when Cycle 3 came out. It is probably still on their website somewhere. Or I'm sure they would be happy to send it to you if you contact them, as Bill suggested.

I just want to point out that I don't think there's any formal guidance on the 5500 issue, but I believe that most practitioners do take the position that if the pre- or same-day merger resolution says 12/31, then the fact that the actual consolidation of assets occurs after that date does not prevent the conclusion that there was only one plan as of 1/1.