Seems like selecting the option to retrieve all of your influence at once, while just below influence cap, will only give you influence up to the cap but still remove all AH entries for which you are owed influence. Essentially if you have more influence in the AH than you can hold and try to retrieve it all at once, you will only receive what you are able to hold and lose access to the rest.
I recently lost somewhere in the range of 10-20m influence while doing this just under influence cap.
Additionally, selecting an individual item to retrieve influence from seems to work normally and prompts the user with a message stating that the influence is unable to be retrieved due to it placing you over influence cap.