If you have completed your submission to HMRC (whether using FBI, EEC or paper forms) and you realise that there were errors or omissions in the data that has been sent, you will need to submit a revised version of the form(s) in which the error(s) occurred.

HMRC require ALL amendments be submitted in paper form

"If you’re correcting a P11D form include all the benefits and expenses for the tax year, not just the ones you want to change" 

HMRC request that you include not only the amended/corrected benefit section(s), but all the existing correct information for the employee as well. For example, if a P11D had data in Section F, Section I and Section M, and the correction is only to the medical benefit reported in Section I, you need to submit a P11D that includes ALL those sections, not just the modified Section I

The modified form needs to clearly show that it is an amendment (traditionally handled by writing the word “Amendment” across the form) and must show the tax year to which it relates.

The P11D Organiser has functionality that will allow you to print an amended P11D which is watermarked in this way, so you can simply make the change(s) to the relevant employee's data, and then using the reporting wizard, select the 6. HMRC Amendments section and P11D Facsimile Amended:-

When you print out this document, you will see that it has a watermark stating "Amendment" across the centre:-

Please remember that a change to an employee’s P11D values may well have an effect on the Class 1A NIC values reported previously during the end of year P11D return, so you may also like to send an updated/new P11D(b) Employers Declaration. 

The forms then need to be sent to the following address with a covering letter to explain the situation (this address changed in April 2022):

P11D and P11D(b) Team
HM Revenue and Customs

The HMRC website detailing this process can be found by clicking this link and viewing the section entitled "Correct an Error".