It seems you have one or more things wrong for 2019.

What does this mean? "tp contributed $6500 traditional IRA 2019 (couple $12000)" There is no Couple; each person has their own IRA account. The 2019 limit is $6,000 if under 50 and +$1,000 for those over 50. Is that a $500 overage or is at least one of these people over 50?

Let's restate for 2019:

"and subject AGI threshold and not IRA contribution deduction."

Means it is not deductible, so that is now part of Basis, or "after-tax dollars."

"Tp converted to ROTH 2019."

If doing all the amount in all Traditional IRA account(s) for that individual, for the total amount, and that was the current year contribution that also was not deductible for that year, that's called "back door Roth." It's a Conversion, and any conversion amount is computed against Total $ in all IRA accounts and Basis, to get the % that is Not Taxable and the rest is taxable.And it should be done immediately, so there are no earnings in that account that were tax deferred.

Examples:

I have no IRA accounts. I open a Traditional IRA, I put nondeductible $6,000 in and immediately transfer the same amount to a Roth, effectively converted as Backdoor Roth. Nothing taxable to report.

Or;

I have $104,000 in total across 3 Traditional IRA accounts; I put in $6,000 not deductible, then I convert $6,000 to Roth. Assuming I have no other Basis except that new contribution:

$6,000 divided by $110,000 (my new total funds) = 5.5% of my total is my basis or "already taxed" funds. That means 5.5% of $6,000 ($327.27) of this conversion is not taxable and $5,672.73 is taxable.

"He got 2019 1099R distribution of traditional IRA"

What was the code(s)? Distribution is not conversions, unless they did a direct transfer or got the funds and sent it on to the Roth IRA broker within the timeframe.

"I prepared 1040 and attach form 8606,non taxable income distribution $6500 subject to basic cost of non taxable income"

Only if that is the Only Money in a Traditional IRA account and there is no other IRA account and there was no money in any Traditional IRA account before that contribution and there were no earnings.

"and ROTH conversion (from traditional IRA to ROTH IRA)"

You need to read the regulations.

"Now I am preparing amended 2018 and saw form 5498"

Which is issued because there was a contribution or conversion. This is money In. That is informational to the account owner.

"and not see 1099R ."

Which is only issued if there is a distribution or conversion or other activity that is money Out. Otherwise, it is not issued.

"Tp said traditional IRA 2018 contribution $5500 (couple $11000). On the 2018 return (tp prepared original) no IRA contribution deduction because of AGI threshold"

So your 2019 info is wrong, because they had carryover basis from 2018 + earnings (most likely). That means a mix of already taxed and tax deferred values to track.

"If he did not convert to ROTH, and keep traditional IRA $5500 ($12000 couple )"

This has to be separate accounts. Retirement accounts are owned by Individuals. Everything is done per person and their basis and amounts are tracked separately.

"as is, then does tp get penalty?"

You can leave a nondeductible amount in a Traditional IRA account, as long as the amount contributed doesn't violate any regulation. But you need to move forward through their timeframe. It seems your 2019 info is not computed correctly because there was basis for that conversion in 2019.

It seems you have a traditional IRA account (or two accounts, which you manage separately for tax reporting) with Basis and earnings from 2018, which by definition makes the 2019 activity a mix of taxable and nontaxable amounts. Example for one person:

$5,500 nondeductible money in for 2018, and at the end of 2018 it earned 10%, so the total of this account is $6,050 and Basis is $5,500 and Taxable is $550 if you convert all of it in 2018. Not converting it is fine. But you track it.

Now it is 2019, and there is a new $6,500 contributed, but this person is under 50. At the end of the year, the account shows new earnings of $1,255 (10%) minus their converted $6,500 = $7,305. Adding back that the $6,500 was part of the 2019 activity.

You have $12,000 basis ($5,500 and $6,500 were after-tax funds contributed) from the total in the account of $13,805 = 87% basis and 13% taxable. So, conversion of $6,500 * 13% means $850 is taxable and the new basis in the account is $12,000 minus $5,650 = $6,350. You keep tracking.

The conversion of $6,500 in 2019 is not that specific $6,500. It is broken out into proportions, for % taxable and not taxable, any time there is Mixed funds (with any Basis) in all traditional IRA accounts owned by that individual.

And that means you have to address that $500 is Over Contributed.

You'll work through the worksheets, which will check your math. I have run the numbers for these examples, but I might have made a mistake. Good luck.