Yes it will. When a donor makes an initial donation of a recurring donation type in PayPal, Total Donations will send information to PayPal about your notification URL. During the next recurring period, PayPal will send a notification to the same URL. After Total Donations receives this message (called an IPN) then it will save data by searching for information based on the custom field. The custom field is a unique number for each donor that Total Donations saves in PayPal’s transaction data.
PayPal allows you to change where reoccurring IPN messages are sent but only for new messages. Past recurring donations cannot be changed after they have been set up. If you change URLs, you’ll need to add a redirect into your .htaccess file so that IPN messages go to the correct place and continue being registered in Total Donations. This is outside the scope of this documentation but a google search on this topic might prove fruitful.