This is a very complicated one. I will propose an answer, but it's by no means definitive. My thinking will evolve as we tease out the implications.
The current position is as follows:
This would overexpose you to the property market and to borrowing. So you should sell one of your existing properties before you buy your new home.
In a rational market, I would suggest that you pay the savings of €120k off your home loan as you are getting little or no tax relief on the interest paid. If you were going to be staying in your existing home for a few years, this would definitely be the right thing to do. It makes no sense to be paying 4% interest on a loan while getting around 0.5% on a matching deposit.
But if you do that, you may not be able to buy your new home for €250k as you will not have the 20% deposit required.
When you identify your new home, you should have matters as simple as possible. Therefore I think you should sell the investment property as soon as possible. To be able to do that, you will need to clear the negative equity.
First iteration:
1) Keep €50k as the deposit for your new house
2) Pay €40k off the investment property mortgage to eliminate the negative equity
3) Pay €30k off your home loan
4) Put the investment property on the market
This will leave you in the following position:
1) You will know exactly what position you are in because you will have sold your investment property and won't be just estimating its value.
2) You will have €50k
3) You will be taking less risk as a fall in property prices will affect you less
In two years, you will need a loan of €200k which will bring your total borrowings up to €420k. That should be doable, given your salary.