Reindexing Results in Lost Composites

[Aaron Bourgoin]

I used the Reindexing button to help organize and synchronize some project files. When I was finished, I discovered that my wall assemblies had gone missing. While reindexing, I did see messages that either said "no problem" and others that said "you'll lose something if you do this" 

Can someone tell me why? or what I might have overlooked as I did this? 

Something similar happens occasionally when I delete and attribute and replace the instances of it with another attribute.