While there is no harm in waiting until year end to reconcile a single 12 months of activity you admit that you already have balanced the account balances each month - that is reconciling - you just have not done it internally in the software. But waiting til year end means you have more to review at that time.
All that reconciliation does is note that the amounts in and out of the account are in balance - where you coded the income and expense has no bearing on the reconciled balance. Only if you change a check's amount or deposit total would you run into an issue down the road. Changing transaction detail will not affect a reconciliation.
