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My configuration disappeared when I updated

Unfortunately, Contact Form 7 changed the way it handles the ID of your form. The CM settings were dependent on the old ID prior to your update. You will either need to reenter your settings, or go in the database, look for cf7_cm_# in the wp_options table, and update the # to the new ID of your form.

Does this plugin allow for an opt-in checkbox

Yes, by including a checkbox tag in the form such as: [checkbox add-email-list default:1 "Add Me To Your Mailing List"]

Then add [add-email-list] to the "Required Acceptance Field" option in the Campaign Monitor section.

Can I submit to multiple lists

Yes, in the List ID field, add all desired list IDs separated by commas.

Can I let the visitor select which lists they belong to

Yes, by including a checkbox tag in the form such as: [checkbox addmetolists "List 1|3126f7e296c347fa53128df941a4f20c" "List 2|1ee18c1ac11ab6eb81624ae1c713a572" "List 3|33dad8d632595e2339b523839fe6d4e9"]

Then add [addmetolists] to the List ID field.

Where is the settings page

There is no settings page specifically for this plugin. Configuration occurs within the Contact Form 7 form administration pages. Each form gets its own configuration.

This plugin doesn't appear to have been updated in a while

Simply put, it doesn't need to. Very little of this plugin relies on WordPress core functionality, and Campaign Monitor doesn't change their API all that often, so unless something is completely broken, updating it every other week isn't necessary.