I'd say you have a couple options that differ by the amount of time required.
Option 1: Export your checking/credit card ledgers from your banks for the unaccounted for periods you mention then import them into GNUcash. They won't be categorized, but it's a fairly simple task to go through and categorize the main ones. Anything else can be categorized in an 'unaccounted for' account and either properly categorized over time at a later date or just left unaccounted for.
Option 2: Make one entry in each of your liabilities and assets that is also part of the 'unaccounted for' expense account, but contains the number required to balance your accounts now. This is by far the easiest and will allow you to start with a clean slate now but keep your prior records in the same ledger.
Option 3: Start a new ledger with the same account/expense structure as your previous ledger. From here on out, you'd open this GNUCash file and start fresh. Also quick and easy but there is no way to look at the old ledger and run reports unless you open that separately. I actually do this every couple of years as a way to force me to clear out obsolete accounts and trim the fat since GNUcash can take a long time to open when the ledger contains many years of transactions.