TWRP 3.0.0.0 Failed to Restore Correctly

I backed up my Nexus 9 and then did a CyanogenMod update, which then lead to me not being able to use WiFi. So I went back to TWRP and restored my backup which was 5GB. It consisted of my apps and games nothing major – but once I rebooted I had no apps or Gapps was like a did a hard reset. So I went and restored a even older backup which I call my baseline backup which is consists of a fresh CM13 and Gapps install, so I had to start over none the less and redownload everything.

Any ideas what went bad? I'm kinda scared to rely on TWRP backup now or to even update CM.

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