Preserve the available application reference, official communications and payment records, and use official account or support instructions to resolve access.
Recover the record without recreating its history
Do not invent a new reference or assume that messages copied by someone else establish every outstanding instruction. Keep the original dates and distinguish documents received from steps actually completed. Work out which of two problems you have, because they call for different responses.
If the account can still be reached and only the email address is stale, this is a change of contact details and the official process for that is the whole answer. If the account itself cannot be accessed, the task is recovery, and the records you preserve are what makes recovery possible: the application reference, the confirmations received at the time, and the payment records showing what was paid, when and to whom. Gather those before starting, because a recovery attempt that stalls for want of a reference number is a delay entirely within the applicant's power to prevent.
Keep everything in its original form with its original dates. A retyped summary of what a message said is not the message, and where a date is the point, a reconstruction is exactly what cannot be relied upon. As you file them, distinguish documents showing that something was received from documents showing that something was completed.