Hi Paco 83,
The Socket 462 on an ATX M/B is rated for only 300 grams for transportation purposes. The Slk 800 weighs in at 505 grams. So "normal" transportation could damage the socket and hence the MOBO. However, I said "normal". Normal like UPS, Fed-Ex, USPS, Mom and Pops, etc. I have the exact same cooler mounted on an Asus board. I have moved it several times with no problems. When I do move it, like you stated, I lay the case on it's side and transport it that way. This way the weight is distributed over the entire mobo and not just the lugs on the socket. One last thing. Since I put the system together, I used all of the standoffs for the motherboard to the case, 9 total I think. I've seen some motherboards placed in cases with only four standoffs being used. You may want to make sure the motherboard is securely and appropriately fastened. If you do take the cooler off, then like the other post stated, re-applying the thermal compound is a must. Cleaning everything well, getting good contact and not letting the screwdriver slip is the real pain in the a**.
I hope this helped,