Something strange happened. My data (2000 entries) were showing up in a portals but there were zero records when looking at another layout based on the same table. I copied it and hit recover and the data reappeared but another table (relatively small amount of data) is missing. What happened? Did this corrupt? Can I avoid this next time?

Yes, it's corrupt. I've seen this with 7, and read about others seeing it. Import that data into a clean clone, if you can. You should think about what you might be doing to cause this. Are you copying files while they're still open? OS Sharing on the FileMaker files? Continuing to use files after crashes or Force Quit (whatever you call that on Windows)? Have you updated to 7.0v3 (that's a good thing)?