Althogh the process might be more complicated than the solution provided below, combining two pools can be a fairly straightforward process.

Determine which Pool is going to survive. Let us choose PoolA and GL account 14100 to survive.  PoolB and 14200 will merge with it.

Reconcile Pool B to bring the FACTS balance to the transferred balance
Make journal entries ( using Allocation and entries or an imported journal entry) to credit PoolB (14200) and debit PoolA (14100) for each fund in the pool to move the 14200 balance to 14100.
Edit and post the journals.
Confirm using a trial balance that the combined assets now can be found in the 14100 account for each fund.
In FACTS confirm that you have transactions representing the "deposit"
If you are planning on maintaining a separate investment account to represent these new assets, create a new account on the FACTS > Accounts tab and map to PoolA. 
If you are merging the assets into the existing PoolA investment accounts, there is no need to create a new Investment account.
When you reconcile PoolA, if you created a new investment account, enter the amount of the transactions moving in as the beginning balance on the disbursements line. Enter the negative value on the investment account holding the "deposit" transactions.
If you didn't create a new investment account, reconcile regularly.

There are many variations of the above, but the basic steps are to make journal entries to move the assets from the closing pool to the surviving pool. Then move the money in FACTS into the correct investment accounts using the disbursement lines and reconcile.