Specifically, there is a question on the application form, "Have you ever canceled or revoked the Russian visa?"
Well, you have
You have, so you must choose the "yes" option. When I completed an application for a Russian visa a few months ago, all yes / no questions where you might need or if you want to provide additional information about your answer offered a text field to do so (this will not appear until you select "yes" to the Question). I can not guarantee that this particular question offers that field, but I would be very surprised if it were not so. Write in this field a brief explanation like this question. The cancellation of a previous visa because they obtained the incorrect dates and issued a replacement with the correct dates will not negatively affect your chances of obtaining a visa now.
Even if there is no field of this type to explain the circumstances, you must still select Yes. Lying in the visa application forms is an excellent way to permanently be banned from visiting a country, especially when it comes to documents issued by the country to which you are applying.