The trade body estimated some 1.9m containers of beer have been left in pub cellars owing to the short notice given to them before having to close.
Operators must recognise health and safety, environmental and economic considerations when recovering casks and kegs.
The guidance has taken into account changes such as HMRC making it possible for licensees to destroy beer once they have received instruction from a brewer.
HMRC said a common-sense approach can be taken to verification and audit of the beer destruction process.
The retrieval of these containers has been restricted by the lockdown measures limiting movement and social proximity. The BBPA said only one person can work in a cellar whereas in normal circumstances this would be a minimum of two.
The guidance has also outlined what forms of verification are accepted by HMRC to prove the volumes of beer involved and that they have been destroyed.
Several operators have published their videos of themselves destroying stock to social media over the past few weeks.
Publican friends... @morningad@CityOfAle@beerandpub@GBPubConfed@EveningNews@BIIandBIIAB Government scheme for destroying beer ...... they require filmed proof.... this is my attempt!! https://t.co/WV3JuT08CFpic.twitter.com/4jdZN7Pecg— Murderers Pub - Norwich (@murderersphil) March 31, 2020
Watch: the moment a publican had to pour £3,000 worth of beer down the drain. Read more about how this Leicester pub has been coping with the lockdown here: https://t.co/DfXOLRmlXl#ukpubs#unitedwestandpic.twitter.com/2Bv7kE2DEp— Morning Advertiser (@morningad) April 23, 2020
BBPA chief executive Emma McClarkin said: “These latest guidelines the BBPA has produced further help all parts of our sector to decide how best to recover containers from pub cellars in a safe and environmentally responsible manner.
“The guidelines should help facilitate the monumental task of restocking pubs in advance of reopening and once lockdown restrictions have been lifted.”