In my view, subject E-way bill cannot be canceled now. For below views, I am presuming that supplier's responsibility was till concerned goods reached buyer and consequently, it is supplier who has to bear losses on account theft & so on.
We suggest to create new e-way bill to bring back the available material (i.e. remaining material after theft) to the supplier (i.e. from place of theft to the place of business of the supplier).
For material stolen, ITC needs to be reversed in accordance with Section 17 (5) (h) of the CGST Act, 2017 by the supplier. For this, it is presumed that supplier is a trader and not manufacturer of the goods.
If you have already issued tax-invoice to the buyer (at the time of earlier / original E-way bill or before that), you need to issue credit-note u/s 34 to the buyer against original tax-invoice.
For fresh movement (after replacement against stolen goods) of original goods from the place of business of the supplier, you need to issue fresh E-way bill along-with new tax-invoice to the buyer.
For the queries / investigation / scrutiny of Dept. in future, above-said documentation along-with copy of FIR & your explanation will be required. Kindly keep supporting statements (for the factual position including various movements of goods, theft etc.) of the concerned transporter also on record.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.