Maybe this is widely known in which case I'll just remove or merge this thread.
When an enemy spy successfully siphon funds, it doesn't deplete your treasury at once, and it doesn't prevent your city from generating income during the mission (since they don't know if it will succeed). However, when it succeeds, the city doesn't generate gold for the next 8 turns. Unfortunately, the interface doesn't reflect this, so your balance goes down even if the GPT is still positive. Tested this with one city, so the effect was pretty clear (my true GPT was just my expenses for those turns).
This is probably why people have reported bankruptcy even though their GPT seems positive.
When an enemy spy successfully siphon funds, it doesn't deplete your treasury at once, and it doesn't prevent your city from generating income during the mission (since they don't know if it will succeed). However, when it succeeds, the city doesn't generate gold for the next 8 turns. Unfortunately, the interface doesn't reflect this, so your balance goes down even if the GPT is still positive. Tested this with one city, so the effect was pretty clear (my true GPT was just my expenses for those turns).
This is probably why people have reported bankruptcy even though their GPT seems positive.