I curious what camera and lens you are using, i've been searching for answers for time lapse color shift for a long time, this is the first time i've seen people talking about it XD HOPE!
I use a Sony Aps-c mirrorless camera, the dramatic color shift happens when shots are unavoidingly underexposed(night condition shadow areas), color shift from green to purple and stuff... it had ruined so many shots until i figured out my best take is to ETTR and avoid composing a lot of shadow areas where there isnt much artificial light, but i'm still curious if this only happens on certain brand like sony?

Also, i don't think reducing clarity will help much, i've looked at the original untouched raw images and they show sign of color shift already, just not so obvious before i do all the editing in LR.

Hi Gunther, would you mind remembering some camera models which happens to have this "sensor defect“? So far Sony nex5t seems to have this problem. Shots that have this problem have one thing in common: night time underexposed shadow area.

I experienced it with the D7000, D5100 - not with the D600, D750, D800. Don't know about 7100, 7200, 5200, 5300, 5500...

Serious Nikon user =P
I see, i'm gonna rent a Sony A7 and D610 for a color shift test before i buy them&find out everything its too late...
but wait, you said it happened on the D7000, D5100, how many d7000&d5100 did you use totally? Is there a chance if each camera will vary from another?

Also, on what circumstances did the color shift happened on those Nikons? I wanna see if there is things in common with this kind of problem, find out better way working around it temporarily =S