The Marketo ID is not modified, however the SFDC ID will change and the lead record disappears from visibility and becomes read-only on the back end. If you are referencing the SFDC lead ID and it has been converted, you may run into issues.
Here is an example:
I created a test lead and the SFDC ID is
00Qd000000fNKfHI then converted it and the record ID changed to:
003d000002Hl6P3I think this may be tripping things up for you.