Okay, so I figured out a work around for when it happens to your save game. If you use the Locomotion trainer with absurd quantities of money (like 999,999,999) to get it down to a number that can be typed into the trainer. (Under 999,999,999) Then you can use the trainer to get it to a point where you can simply take out a loan to get positive cash flow, and continue as if nothing happened.
I recommend pausing the game during this process since none of it un-pauses the game.
In step form
1. Set trainer to 999,999,999 money in pounds.
2. Load affected save file.
3. Use Money Cheat in trainer to get the amount below the 999,999,999 mark.
4. Take note of the exact amount you are negative, (Let's say it's 502,222,189).
5. Save, then exit game.
6. Enter an amount just under the negative amount into the trainer. (So, 502,22,170).
7. Reopen the new save.
8. Use the money cheat once.
9. Take out a loan for the remaining amount, putting you into the black/positive money.
10. Continue normally from there.
Anyone who stands in the way of change, is out. ~ The Navigators (2001, UK)