Seeing as this is a first for me just looking at this issue, let me try to understand the situation.
My Understanding
Given that you backed up your saves and everything, FBI manager is giving you errors and you can no longer read the saves.
Proposed solution
1. Use the backup and restore your 3DS to it's before state and try again.
2. Try playing with a backed-up unmodified version before trying this again to ensure everything still works eg. no data loss
Further Questions
- Which region game are you using? (EU Birthright, USA Special etc.) Given that you are using an iso or internet download, is it possible that the game file was corrupt?
- I am confused as to how you are able to use the toolkit on the game and not have any files extracted. I suspect the .cia you are trying to extract is corrupt in some way or the toolkit is not in the same directory as the game file. Are they in the same location? (eg. both on desktop or both in documents)
If
@KunoichiZ has a better understanding of the situation, my interpretation may shed some light on the situation.
Hopefully what I proposed helps.