Installed CM12.1 after TWRP backup-restored but missing data

I did a backup of all partitions with TWRP and installed CM12.1 20150907 nightly to have a look (coming from stock Lollipop). The exchange services kept crashing and wouldn't sync my contacts so I decided to revert; I wiped everything and restored from backup. When the phone was back online I found that there was quite a bit of data missing from internal storage. I went back into TWRP, re-wiped everything, formatted internal storage, and restored again but still found data was missing.

Did I miss a step somewhere? I have just about come to terms with my information being irretrievable but I'd like to be prepared for next time.

Thanks in advance.