They'll appeal most likely but their chances of success look slim.
Right now Apple is probably winning a battle but might be losing the war. The next big EU mandate, besides tackling climate change, will probably be clamping down on tax shenanigans.
Next time they won't even be able to win anything as the law will be explicitly against such corporate maneuvers.
In most cases, a veto can't happen unless the following conditions are met:
1) Less than 55% of total Member States (less than 15) voting
AND
2) The voting Member States represent less than 65% of the total EU population
AND (assuming at least one of the conditions above aren't met)
3) At least four countries vote to block the measure
OR (if not all countries are voting)
4) The minimum number of countries that represent more than 35% of the total EU population, plus one country, vote to block the measure.
This prevents e.g. 3 big countries from blocking the others.
For instance, the Netherlands announced a withholding tax on royalties for 2021 "for cases where abuse is involved" [1] after international pressure. The way I read this is that they are building a facade where it looks they are complying with other EU regulations, but in reality it's business as usual. This way other EU countries have no appeal to these schemes as the Netherlands can say "we looked into these allegations, but no abuse there" and do nothing.
[1] https://www2.deloitte.com/content/dam/Deloitte/global/Docume...
However, the reality is... realpolitik still exists. If Germany and France decide things should really change, what negotiating power do you think the Netherlands or Luxembourg or Ireland really have?
For example the Dutch economy is basically hitched to the German one, Germany can find a lot of creative ways to inflict a lot of pain on the Netherlands if it really wants to ;-)
[1]Seems I was wrong about this