I'm not sure why you think that Waterloo is close to Ypres, they're about 100km/62 miles apart. The closest battle was at Charleroi, about 30km/18 miles away from Waterloo, still enough distance that Waterloo was not affected.

The battlefield had the main damage done to it very shortly after the 1815 battle when King William I of the Netherlands (which at that time still included Belgium) ordered a large mound, Butte de Lion, Leeuw van Waterloo, or Lion's Mound, constructed on the site where it was believed that his son, the future King William II, had been injured during the battle. This construction, 43m (141') in height and 520m (1706') in diameter was completed using earth from around La Haye Sainte farm and a sunken lane which had both featured in the battle. The Duke of Wellington is reported to have said "They have altered my field of battle!" Also, as parts of the battlefield were (and still are) farmland, they have been somewhat churned up by subsequent ploughing etc.

EDIT: Just thought I would mention, the battlefield is a tourist attraction these days (and was pretty much immediately after the battle). One can have a guided tour of the battlefield, climb the Lion's Mound, visit the Waterloo Panorama, the Wellington Museum and Napoleon's headquarters reasonably cheaply if you wish.

I visited the field last year--very well preserved, definitely worth a look--but I couldn't help but laugh at the idea of the "Lion's Mound" being raised to commemorate a noble's wounding. Just imagine if they had raised a mound for each common soldier who became a casualty that day!