I have a couple of suggestions.
1.) Under Preferences -> Advanced -> Playback Statistics, enable automatic synchronisation of file tags with statistics. I'd recommend using this alongside External Tags too personally, so that you aren't constantly writing plays or ratings to actual audio files. Some audio formats won't support arbitrary tags so you would need External Tags for those anyway. Then if your foobar2000 library goes kaput again in future, it's a simple job of re-importing stats from file tags. I inexplicably lost stats a few times in the early days, so this is my way of taking matters into my own hands.
2.) This means you will want values in your file tags and library to remain consistent. Ordinarily they should be, but sometimes they won't because of last.fm pulls (especially if you also scrobble from mobile), or foobar crashes (maybe not as much of a problem with newer foobar versions), or maybe other reasons, so rather than having separate columns for a bunch of redundant playcount columns, my solution is to have one master playcount column which produces fat X and arrow symbols when there are inconsistencies, and toolbar buttons for moving stats & last.fm plays to tags, and importing from tags to stats, whichever the case required. There's probably a more elegant way to code this but it works.
Ideally what I'd also like is an autoplaylist populated with just these inconsistent items (so that I can keep track of them and fix them), but haven't figured out how to do that yet.