Though it may look a little strange that batch 1 started late February, this will not cause any harm.

The Fiscal Year End date will not change regardless of when you run Yea End.

If you are on current versions of Adagio and assuming you haven't purged recent history, then the "Calculate as of" option will give you the correct balance back dated to your actual Fiscal Year End date. YTD totals come from the Transaction reports which allows you to set the date range.