Question: My CPU cooler is too big so i cant get my motherboard out to clean it it's like 7 years old and I need to get the dust out. I have tried to take it out without taking off the motherboard but it doesn't fit.

Answer: 
Yes, you should replace the compound if you remove the heatsink.

Thermal paste is generally either a near-fluid or putty like compound when applied. Over time it "sets" into a solid due to heat and forms an effective seal between the CPU case and heatsink.

When you remove the heatsink you break that seal and create gaps in the compound. As the compound is no longer malleable it cannot reflow into gaps when you refit the heatsink and can easily end up with air bubbles and poor contact between the CPU and heatsink.
Why remove the heatsink?

Purchase an air duster (compressed air, or a blower designed for the same role) to blow the dust out of your case. Less work involved, and no need to worry about damaging your system\*

\*don't blow the fans - preferably hold them in place while cleaning. This prevents them from spinning up and acting as a turbine generating power.