Hi lindawild,
Since this is your first post in the Community, I'd like to give you a warm welcome.
Removing transactions from a reconciliation will affect your general ledger. It's often suggested to void a transaction compared to deleting it. Voiding a transaction allows you to keep record of the transaction but it'll have a zero amount.
Removing transactions will impact financial reporting, such as deleting/voiding an expense will reduce the spent amount for the account. However, ensuring that the correct transactions are included in a company file will help to ensure accurate books and reporting. For more information about voiding and deleting transactions, check out this helpful article: Void or delete transactions in QuickBooks Online.
If you have further questions, don't hesitate to reach back to me. I'll be happy to assist. Otherwise, have a great rest of the week!