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Could you tell me which tense is correct in indirect speech?
Also, could you please explain the reason?

We told Sharon that her comments don't really relate to the key issues at hand.
We told Sharon that her comments didn't really relate to the key issues at hand.

Thank you.
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>We told Sharon that her comments didn't really relate to the key issues at hand.

is correct.
I think, the direct speech sentence is in simple present: "Your comments don't relate to the key issues."

When the "introduction"part of a sentence in indirect speech is in a past tense form (here: "We told...") the actual tense in the following sentence has to be backshifted.

The rules:
DIRECT speech tense -----shifts back to ------> INDIRECT speech tense:

Present (Progressive) ---------------------------> Past (Progressive)
Past (Progressive) -------------------------------> Past Perfect (Progressive)
Present Perfect (Progressive) ------------------> Past Perfect (Progressive)

will-Future (Progressive) ------------------------> Conditional (Progressive)
will-Future Perfect (Progressive) ---------------> Conditional Perfect (Progressive)

Past Perfect, Past Perfect Progressive and the Conditionals cannot be backshifted!
If they occur in a direct speech sentence, they remain the same in the according indirect speech sentence.

Examples:
"I cannot tell a lie" ----------------------> He said, (that) he couldn't tell a lie.
"We are not amused" -------------------> Queen Victoria said (that) they were not amused.
"I came, saw and conquered." ---------> Cesar said (that) he had come, he had seen and he had conquered.
"I went to London." ----------------------> He said (that) he had gone to London.
"I will go to school" ----------------------> He said (that) he would go to school.
"I am eating." ----------------------------> He said (that) he was eating.
"I would never visit her." ----------------> He said (that) he would never visit her.
"I had seen her before I came here." --> He said (that) he had seen her before he had come there."
...
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The rule says that the verb has to be changed in reported speech because you refer to an action in the PAST, something it was SAID. In this case, Sharon "made" comments and you are reporting it.

Sharon:
A and B: Your comments don't really relate to the key issues at hand.
[...]
C: Hey, what did you tell Sharon? She looks frowned.
A and B: We told her that her comments didn't really relate to the key issues at hand. She didn't like it, I guess.

BUT, when you report facts that are ALWAYS valid, you can use simple present tense.

Hey Mom, our teacher told us today that oil is lighter than water.
... oil is and will always be lighter that water.

Mary told me she doesn't like roses.
... she doesn't now and maybe won't forever.

Hope this helps! Emotion: smile
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Comments  
I would say that the last one is " He said (that) he had seen her before he had GONE there.
 Raul's reply was promoted to an answer.
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Thank you for helping me Emotion: smile

Tense is not so important in my mother tongue, so it's hard for me to understand the concept.
I have been studying to build up my vocabulary, and I found a couple of indirect speech sentences in my text book. That one was one of them.

Here is another sentence that I can't understand why present tense is used;
"The doctor suggested that I decrease the amount of medication."
Why "decrease" is used here?
According to your explanation, I think "decreased" should be used.
Could you please help me with this one?

Thank you!!
>I would say that the last one is " He said (that) he had seen her before he had GONE there.

Nope, you mustn't change the verb in indirect speech!
You only change the tense, and if it doesn't fit anymore, also the adverbials of place, time, etc.:

Peter (on the 22nd in London): I came here yesterday.
Jeff (on the 31st in New York): Peter said he had come there the day before.
>>Here is another sentence that I can't understand why present tense is used;
"The doctor suggested that I decrease the amount of medication."
Why "decrease" is used here?
According to your explanation, I think "decreased" should be used.
Could you please help me with this one?

Actually, you're right - it should be "decreased".
Check again that sentence in your book, maybe the introduction says "The doctor suggests that..." or "The doctor has suggested that...", in these cases (i.e. with a present tense introduction), the tenses are not shifted back in indirect speech but remain the same.
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