This was also the solution for us, thanks!!! We have SQL 2008 R2 and ArcGIS 10.3.1. I did just loke Kevin mentioned, copied and pasted the feature classes into the same dataset, and changed the keyword to SDEBINARY. Then I deleted the old feature classes, renamed the new ones. I also used the batch create spatial indexes since those were gone, but the attribute indexes copied over fine.
I also noticed that this improved the performance when SELECTING features, especially annotation.
David