After some digging around, it seems quite a few have had this problem before. And it seems dev intervention is the only way to fix it.

I'll admit, I did stop playing for a while, plus I went offline and online a few times (back in the days when switching didn't set your resources to zero).

Colony 'website':

I had a look and my old charter code (the time I went offline and back online again) was h6Esyb8I