There should be an expiration date for when final invoices should be submitted. Granted the assumption is no outstanding claims, contractors should be required to submit their final invoices within a certain period (say 6 months or whatever makes sense given the contract type and ), or else they forfeit the final payment and the contract is closed. Failure to return property within certain time restrictions results in penalties, etc.
Assuming that the delay is the contractors fault, they need to be held accountable. Regretfully, the delays are not usually because of missing invoices, but rather because of outstanding issues with rates, especially with continued issues with perceived unallowable costs.