Dayaj'a' should never mean, "Did he/she/it understand?". The prefix Da- means that the grammatical subject (the person/thing doing the action) must be second person singular ("you") and the grammatical object (the person/thing the action is done to) is third person ("he/she/it/they"). To get "Did he/she/it understand?" you would need to have a null prefix (the absence of a prefix really, but for consistency in talking about prefixes I prefer to treat it as a silent and invisible prefix) which would give us yaj'a'. Note that your other suggestion "Do you understand?" has a second person subject ("you"), but doesn't have an object at all. This would be represented by the prefix bI- as in bIyaj'a'.
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Why can't this mean "Torg, don't you understand Mara?" If Klingon has no verb tenses as I understand them (and I've studied many different languages) why aren't those translations accepted? I would want different tenses in Latin (as a Latin teacher) or in English, but I am confused about Klingon verbs.
Why can't this mean "Torg, don't you understand Mara?"
Because there is no -be' "not" in the Klingon sentence.
You can translate it as "Torg, do you understand Mara?" if you want -- present tense but without the "not".
n't you understand Mara?" would be torgh, mara Dayaj