It is unlikely you will get compensation, and the sad reality is, all builders and strata managers will tell you that planter boxes will fail, cause damp etc, and push for their removal. The EC also need to maintain the building, and getting the builder to pay for it is certainly sound financial sense. Also, there is no way of satisfactorily fixing inbuilt planter boxes without removing the contents.
For your predicament: are these trees visible to other areas of the building (especially common areas)?
If so, then you can argue that the amenity of this has a material value on the price of all the units which will be difficult to replace. The usual number bandied about by real estate agents is that mature, healthy plantings add approximately $5K to the sale price; this may or may not translate to $5K per unit, but it is a start.
As you say the builders warranty is almost up, the trees would have been in situ for 7 years, and, assuming they were purchased as semi-advanced specimens are probably no more than 10 years old. In other words, what you are about to loose cannot be replaced in under a decade.
There is good news: as the trees have always been in a planter box, they can be relatively easily transplanted. It is also autumn, which is the prefect time to move large plants. Having explained the value of the trees to your EC and the other owners, I would ask the EC to get an professional arborist in ahead of the builder to prune the roots and prepare the trees for transplant. Then, get the EC to build a new non-permanent planter box over the newly sealed, tiled area, and that will go some way to solving your issues.
If the EC don’t agree to this, then you will need to drum support up within your building to get the OC to force the issue.