That can be explained for reasons other than their support having fallen.

Portugal doesn't have any significant anti-EU feeling, probably because Portuguese Nationalism doesn't have the kind of delusions of grandeur (i.e. the "we're better than other Europeans" beliefs) that you will find in the Nationalism of the larger European countries (and which was very much what propelled Brexit in the UK) and hence the local Fascist far-right (Chega) don't really sell that specific type of fable whilst the ultra neoliberal far-right (Iniciativa Liberal) think leaving the EU would be "bad for business and hence bad for the business elites" (which is entirelly what they're about).

Since a lot of the electorate of the Fascists are old, backwards and quite ignorant people who really don't follow or care about anything outside Portugal, it makes sense that in the absence of an anti-EU message from their party they would simply not care enough to go vote in EU elections.

Meanwhile Iniciativa Liberal, the other far-right party, are far more Technocratic and internationalists (their politics are literally importing a version of the American model on steroids - one even more Reaganist than Reagan - to replace the European-style social safety net) so their voters are just as much or more likely to vote in the EU elections as everybody else and hence they've actually increased their vote a lot percentage-wise (more than double) and even in absolute terms (12% more votes than in the last Parliamentary elections, which had a lot less abstention than the EU elections).

I wouldn't call this good news, though I definitelly agree with you that people are making "a bit more of a distinction between national and EU elections".