This has happened to me several times, and I wish it wouldn't do this. I turned off automatic updates, because it seemed like an update would happen at the most inopportune times, following by a lengthy indexing, which rendered my computer fairly worthless until it finished. So, now, I wait until I see that a decent-sized update is available. It downloads, then says "preparing library...". Following this, it will start indexing, after telling me that resources will be added the next time I reboot. I wait for the indexing to complete, then restart Logos. The new resources are added, but now it'll start indexing all over again. Arrrgghhh! This can be very annoying when you're trying to get stuff done, but the computer is very slow.
I know that the power and speed of the searches is due to the indices, so I'm just ranting a bit, but I do wish there were some way for the indexing operation to be sped up. First world problem, right? I am grateful for Logos and all it does for my Bible study.