I understand that this is an old thread, but I am suddenly experiencing this same problem in version 1.12.0.3140 (WindowsPlayer x64) en-us. I played KSP for some time on my old laptop and never experienced this issue, then I got a new desktop and the first time I play, I run into this problem. I found a Reddit thread that also discussed this issue and a user recommended de-selecting the "Tidy up debris cluttering KSC" in the General Settings. As soon as I de-selected this setting, I was able to recover my craft just fine!
