The Joker’s past in the comics is often portrayed as multiple choice; perhaps Jeremiah’s memories of before his fall into the chemicals will seem multiple choice to what’s left of his mind.
In fact, perhaps Gotham could go the DC Comics route of even the Joker not being entirely sure which version of his backstory is true.
Well, it stands to reason that a fall in a vat of chemicals could be enough to alter Jeremiah’s mind to the point that he forgets a great deal about Bruce Wayne.