The Mass Add / Delete feature in the File Maintenance tab in the GL is designed to add or remove the GL accounts associated with the fund classes identified in the Master Chart of Accounts. Therefore, if a GL account is not being added or removed for a specific fund, it is possible that the fund does not belong to one of the classes associated with that account in the master chart.
To determine if this is the cause of your issue, check the Master chart of Accounts Maintenance. Are all the fund classes that need to be added or removed associated with the account number? If not, then either add the fund class temporarily and rerun the GL Account Mass Add/Delete process again or manually delete or add the GL Accounts needed.
If you are removing the accounts, perhaps the purge unused GL accounts tool will better suite your needs?