She does NOT deal with TNers on an everyday basis. They deal primarily with marriage-based immigration, and H1-B based immigration, both of which have far different leeway and forgiveness than TN/TD. And they deal with folks that are not likely to want to cross the border to Canada regularly.
You can file I-539 for him, but that would start HIS 90-day clock over again. the 90-day rule states that you cannot do anything "different" that what you intended to do when you either entered the country of filed for a particular non-immigrant status (like TD) for 9o days. of course, he would have had to have been in US on the day you submitted I-129/I-539 and stayed in US.
If he had entered on B2 (as I believe I suggested back on January 2) then he would have been fine, but you said he is "under" your TN, implying he has TD status and entered on it. To have gotten a TD based on your expiring TN merely put him in the same hot water you were in until you filed I-129. Getting a 3-month TD instead of a 6-month B2 when you are facing a 90-day clock is not the best timing.
Like I said, you are in a situation where you need to either (1) file I-485 together before the 4/28, or (2) have him file for TD, or go back to the border and get TD based on your new TN, and then wait out a fresh 90-day clock, or (3) YOU file as soon as you can, and he files as soon as he can, after he gets new TD.