It is often a time problem here (past and presense). If there are two possibilities did and do, I will translate do because that means nechápe. If there would be Standing on to nechapál i would translate it too with a paste tense, that means did not understand it. So my Question is, if the have an English sentence with a past structure (he replied), where should/must be Always a past tense too in the second part did not understand instead of do not understand, even when in the Czech sentence is used the present form nechápe and not nechapál?
English reported speech most often uses backshift in the sequence of tenses
Czech does not do this. If the speech was in the present tense, the reported speech is present as well. For this reason, you cannot expect that the tenses will be the same in Czech and in English. They will be the same in those cases, where English does not backshift.