Regarding your first question, there are many caveats when it comes to retrospective VAT reclaims, I would check with your accountant just to make sure. If they are eligible you should just be able to enter the invoices with that specific rate of VAT and it will get picked up on the return (just check your backing report to be certain).
Yes generally speaking, applying the reverse charge option should be sufficient. There’s a section here in the VAT return regarding this. Just bear in mind that QF will treat all EC acquisitions as if they were goods not services. If they are services you will need to manually adjust some boxes for now (see here for more details).
Yes you can changes them without needing to delete and re-enter.
Hope that helps!