this problem is solved for me atleast . i had installed some mods manually and some with NMM .i wanted to install all my mods with NMM .so ,i uninstalled all the mods with NMM ,removed the manually installed mods .added those mods to NMM .then i re-installed all mods back with NMM . that's the point i started getting many weird bugs .like bounty for nothing , aspect of peryite coming up (nothing works except the console) and my saved item in a custom house gone even though i hadn't touch that mod. i tried loading all the save files but the same thing .so ,i tried to reverse this back ,such that my skyrim data folder got back to it's original structure .i had made a backup of data folder before touching it. i used wrye bash to see what mods do the old save file depend on.after 2days of trying with so many CTDs and reordering the loadlist according to the save file.i successfully loaded my old save file and all those problems were gone. so my suggestion is to use an old save file with the mods installed that were present at that time. use bash to see those mods.