It would cause the EU to waste time trying to fix the situation. Either the UK's MEPs would be forever elected out of step with the rest of the EU, which would be annoying and costly (due to having to do two lots of inductions), or rules would have to be changed to shorten that one term for British MEPs to re-sync.
The EU is strongly against not participating in the elections but remaining in the EU past that date for other reasons too, mainly that it would be undemocratic and unfair to British EU citizens who would be unrepresented.
Also note that while the elections take place in May, the UK would have to indicate if it will take part by April 12th to allow for enough time to organize things.
Update: According to legal advice by EU lawyers the failure of the UK to elect MEPs but still be a member by June 2nd could cause "paralysis" of the European Parliament. It seems that legally it would be difficult to proceed with one member state being unrepresented.