Withholding tax on net withdrawals or for withdrawals in-kind are based on the grossed-up value of the de-registration. For example, a net deregistration of $5,000 (in which you want to receive $5,000; or have $5,000 in a security you wish to withdraw) would result in 20% WHT, plus the $50 partial deregistration fee and tax. So the result would be: $5,000 / 0.8 = $6,250 + ($50 + tax).
You can submit a de-registration request either online or via the RSP Deregistration Form.