If I have a user who encrypted a file and has now left the company is there any way to recover the encrypted file? –No way to recover the encrypted file(if the employee left the company). AxCrypt will allow the users to decrypt the encrypted file with the original password which is used for encryption.
If you know the file password(which was used in the file encryption process) to decrypt/open the encrypted file. Otherwise, Without file password nobody to decrypt the encrypted file.
If not, what can I do to protect company data should a user leave? –If the employee leaves the company, please ask the AxCrypt account password or decrypt the all encrypted file. After that, you will change/reset the account password then encrypt the file.