"Is it ok to reduce cash balance at the end of the year for that amount and enter net amount?"

Isn't that what happened?  The balance sheet should reflect actual numbers as of the year end date.

correct,it is what happened 

I was just wondering if we manually enter net amount (cash less loan repayment) or software(Proconnect) calculates it after you enter it in shareholder info but it did not unless I am missing something

I don't do ProConnect but if it didn't transfer the loan info, the odds are pretty good that you have to enter it manually.

Thank you for help