Flat rate VAT

A new VAT registered client has been using the flat rate VAT scheme but it seems that they didn't realise that they had to apply for it.  They have only sent in one VAT return and are now half way through their second quarter.  Does anybody have any recommendations?  It would cost them circa £2500 if they had to recalculate at standard rate VAT and use Standard VAT until the third quarter.  How hot are HMRC on applying for the Flat rate scheme?  Would you recommend sending off an application now and back-dating it?  Thank you