Mangled profile

I feel like a noob, but here goes.

I have a version of TBP that I use on my main desktop. At some point, I must have hit "Update" and now have mess. I know how to transfer a profile from an installed to a portable version (copy profile) but it seems that some of my information is in the portable location, and some at the "Application Data" location. Copying either makes the new portable version act like a new install. Does this make sense? (Be kind.) Is there a way to save this, or should I just use this as an opportunity to migrate to TB 3.0?

Thanks in advance for any help