Correct. Award bookings are never charged a partial number of miles when you make a change. If you had an award booking that cost 60K which was booked on July 1st, and you change it on August 1st to different flights/class that cost 90K, then you should see 3 entries on your statement :

August 1 - Charge for 90K miles
July 1st - Credit for 60K miles
July 1st - Charge for 60K miles

The total amount in that case would be correct. The sequence of events/dates obviously isn't (the refund really should be August 1st, not July 1st), and as there isn't even a PNR mentioned to make it easy to track them - and because the refund posts with the old date it's easy to miss it. It's not 100% clear if that's what the OP is saying happened or not, but the 90K miles charge they mentioned is correct.

Taxes and fees (if any) are different, and are done as a credit/charge for the difference between the old and new prices.