I have just spoken to someone who works for the government and asked what the affected pilots should do. His answer was to write to your MP, even if you don't live in the UK. If you have property include your address in your letter of protest.
Also mention that the Transport Ministry has in some way admitted some degree of error, in that they admit the CAA's 'guidance was in error'
Time is short, even if it's just a couple of paragraphs it will help. The change.org page can also be copied and pasted.
FM.