Your temporary absence form Greece will not be a problem for the time being.
What is the physical presence requirement for Golden Visa holders who want to apply for Greek citizenship?
My family got our Golden Visas two years ago through property investment in Athens. Our goal was to apply for citizenship after seven years. We return to our home country before Christmas of 2019, then the coronavirus hit, and we were not able to return to Greece. We have been away for almost six months. We are worried that this extended stay away from Greece might impact our ability to apply for citizenship.
This can delay a bit your application for citizenship, In order to apply for citizenship, you should live seven years continuously in Greece, which means that you should stay in Greece for 10 months each year.
Τhere is no reason to worry about this issue. The coronavirus situation is a force majeure phenomenon globally. There is no need to prove the existence of the above situation. According to existent jurisprudence, the periods of such force majeure situations are not counted in the finally calculated periods of absence. From the passport exits/entries, it is proved that it was not possible to return on time.
Physical presence is essential as far as the application for Greek citizenship in general. Acceptance or denial will not be justified otherwise could be subject to appeal.