So QB is saying these five transactions have been deleted, which has thrown off the beginning balance by over -$50,000 when reconciling. 

When reviewing these transactions figures, I can still see the exact amounts in the account reconciled — they haven't been deleted?... It appears these transactions were transfers between two accounts in QuickBooks, and I’m wondering if that might be the issue. Perhaps they were marked incorrectly or removed from one side of the transfer?

I’m unsure whether I should re-upload them or leave them as-is, since I can already see those exact totals of the 5 transactions still reconciled in the account? 

I am confused on what I should do?