I don't see how the employee could claim anything if he wasn't taxed on it in the first place. Subsection 5(1) of the Act is very specific in establishing that only the amounts received by the taxpayer in the year from employment are to be included as income. Note that I said "received"; not income earned. The fact that the employee only received $4,000 instead of the $9,000 he was owed is unfortunate, but the T4, if it had been issued, should only show $4,000.
I imagine no T4 was issued at all, or if it was then it should not have been, since the employer did not actually pay the employee anything. WEPP payments fall under subsection 56(1)(r) which established that this is taxable income in the form of earnings supplements. The bottom line, therefore, is that the employee only reports $4,000 of taxable income so there is no loss in wages to claim as the unpaid $5,000 is not taxable under any subsection of the ITA.