@Charm25 

I don't think your questions were answered.  

"1. The books until october 2023 were closed, will it affect the transaction records?"

If you change the merchant fee entries before 11-1, it will indeed change your closed periods.  It will move the cost from COGS to Merchant Fees expense.  Net income will be unchanged, however.  You can make a single adjusting entry at each month-end (or each day or week depending on how accurate you want this to be) to move the cost from COGS to Merchant Fees expense.  If you want to do that, create a journal entry: debit Merchant Fees expense and credit COGS on the last day of each month/week/day for the total.     

"2. Should I create new expense account for merchant fees? If yes, my concern is that the 3rd party was mapped to cogs and dont know how to change it."

Ahh, got it.  I guess your options are to create a month/week/day-end journal entry as described above, leave the fees in COGS, or figure out how to change the mapping if possible.  If you can't change the mapping and you definitely want to track the merchant fees as a separate expense, then the month/week/day-end journal entry is really your only option.  

"3. What will be the effect of the transfer?"

It depends on how frequently you make the adjusting entries.  If you make a month-end adjusting entry, then any reports that are run with an ending date other then month-end, will have the merchant fees in COGS.  The same applies to weekly adjusting entries.  It depends on how accurate you want the financial statements to be and how much effort you want to put into making them that way.