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But I would like to use JS to grab all of the recordID's that need to be deleted and then somehow get them over to a php script.
Any guidance would be greatly appreciated.
Then for each click of a checkbox: add message no. to some array.
When submitted: send array as query string (delimited by whatever). Delete each message, then, when you get a successful server response, loop through array again and do id.innterHTML=""
Table rows may not be the best because they may leave an space when empty (depending on your table style). Perhaps <div>'s with <span>'s would be a better option, with the id on the div.