I have the same issue.
What happened is the following:
a) attachments show up under different thoughts
b) attachments dissapear from a thought but are apparently still there because if I want to re-attach them, I get the message that this link is already there and if asked to go to the thought with this link it is the thought where the attachment is missing
c) cross linked attachments. Two thoughts now share the same attachments. If I delete the attachment, it will dissapear from the other thought as well.
I hope it is possible to clean up this mess. I am quite surprised by the level of corruption of the database.