Reconciliation

Yes, when you reconcile the beginning balance is calculated as the sum of all the reconciled transactions in the account from the beginning of time. If you change the amount of a reconciled transaction, or delete it, then the opening balance will change.

If those checks and journal didn't clear the bank account, then they shouldn't have been marked as reconciled. In this case, there must have been one or more prior adjusting entry made to balance a previous reconcile, which is (IMO) a terrible thing to allow in your books (if you can't reconcile, then your data is wrong.)  I'd try to find those adjusting entries in the account and consider deleting them. If it/they are recorded using the net amount of the transactions you deleted, then everything will be fixed.

If those checks did clear your account, and so no adjusting entries were made to balance the account, then they shouldn't have been deleted and should be added back to the account. You can manually mark them cleared or add them to the next reconcile or create a special small reconcile with only those checks, where the ending balance you enter is the same as the beginning balance of your current bank statement.