I had the same issue. You could open the save game in notepad++ and Ctlr F then search for the "crawling". Just change it to "walking" for every instance it shows up and it should fix your problem. As long as they are no longer wearing the handcuffs that is.
Viewing post in Aric's Expansion Rebred
If you change every crawling to walking you just temp force fix it , and possibly let even cuffed slaves to walk thus they can escape and wings+flying etc are changed to walking to. The problem seems to be that the cuffed status is permament and slaves keep it even after removing cuffs/equipping different equipment to the same slot and advancing a day . With only a few slaves and small save you possibly can change restrained to none restraints to free , but i can only hardly see wich part of the code goes to wich slave /i have 10+/ so there are possibly some other things that force keep the cuffed status , thus crawling.
edit : needs a bit of testing , but it looks like it changes the movement trait too so even after editing restrains and restrained it still keeps the crawl, i let my eyes rest a bit and try to dig a bit more in the save
edit 2 : Yepp it seems that cuffs set both movement and movement trait to crawling and the 2nd makes it permament . Code seems to show in mod effect settings that the change in both is intended , but maybe there is somethings that should check and change it back if cuffs are removed , but me to find that its a bit too deep.