Does what I did, repeating the second year of preparatory classes, with unregistered absences exceeding the permitted limit, constitute a form of deception that renders the money subsequently earned from work unlawful?

Fulfilling trusts and observing administrative regulations that do not contravene Islamic law is obligatory. Therefore, it is not permissible for the institute's professors to be negligent in recording student absences, nor is it permissible for students to seek to prove their attendance despite their absence.

Regarding repeating the second year, as long as the recorded absences permit it, there is no harm upon the questioner concerning the permissibility of the salary if he completes his studies, gets employed, and performs his work as required. The questioner is advised to seek Allah's help, excel in his studies and work, and abandon obsessive thoughts.