"I can't think of a situation where I would recommend a SIMPLE-IRA, there's nothing simple about them."

They are great for small companies, and especially I like to allow employees to chose their own account brokerage under the plan. That's why.

2 year rule:

https://www.investopedia.com/ask/answers/05/simplerollover.asp

"Employees must wait two years from the time they open a SIMPLE IRA account before transferring those funds into another retirement plan. If you withdraw money from a SIMPLE IRA during the two-year waiting period, you may be subject to a 25% early-distribution penalty."

Notice that is open the account, not leave the job. Similar to why you are encouraged to open a Roth, even just to let it sit, because that starts the exclusion period clock ticking.

"then personal investments which this 1099 personal IRA"

So this conversion was made from a Traditional IRA...

"but would they have done 2 1099's one for the conversion and another for the amount she did not convert"

Not necessarily. For instance, if the entire amount was transferred (direct) and not fully deposited into a Roth at the other end (the other part went to new Trad IRA, to withholding or to disbursement to your client's personal account), the issuing agent would still only send one 1099-R. They don't know where the money went after they sent it; they only report on the 1099-R that they Distributed it per the owner's direction(s). That's why there is a code for "early, no known exception." Because they might not Know. That doesn't mean there is no exception.

"Ask if she did a "Back Door" Roth - Make a non-deductable IRA contribution and the investment advisor immediately does a Roth Conversion for the non-deductable IRA contribution.

Since no deduction, there is no tax on the conversion"

Unfortunately, that won't be true for this person, unless their Trad had no earnings all this time and no basis, either. What you are describing is Basis, or Post-tax:

"The pro-rata rule is used to determine the after-tax amount of a Roth conversion when the taxpayer has both pre-tax and after-tax balances in their IRA(s). Company sponsored plans like 401(k)s and 403(b)s are not used in the pro-rata calculation, unless rolled over to an IRA in the year of conversion"

Putting a nondeductible contribution into a Traditional IRA as a step towards "back door" Roth is fine, but otherwise, is no different than any other Conversion, and follows the conversion rule for ordering, for tax determination. What makes it "backdoor" is immediacy and not other pre-tax holding(s) to compute pro-rata against. No Earnings on it or in the account(s), when converting, is what makes a Non-Taxable conversion. Otherwise, it's pro-rata.

"the fact that the 1099 was showing more than what they were calling a conversion."

That just means your clients don't really understand any of this, and I have seen lots of brokers getting it wrong. You are looking at Distribution. That can be sent as withholding, transfers, conversion and even in her pocket. All of the above.

"Plus he stated in his letter to me he sold some stocks at a loss to minimize her tax burden from doing this conversion."

OMG; she needs to go to someone else. Conversions are by $$. There is no Gain or Loss netting against anything. All he did is convert holdings to cash, locking in that investment's reduction, within that account. Sheesh.

"I have to talk to him and get the full story and why it was coded as an exception to penalty and she is not old enough to have the penalty waived."

There is no penalty for Conversion, but there is for any withholding, unless they make it up in the rollover/conversion; and the amount she kept is subject to penalty. You would need to follow the money, to know the amount withheld and the amount she kept, because that is the Early Distribution, then.

And it's all subject to income tax, as described.

"I can see all kind of ideas he may have had. You make the contribution to the ira then convert to roth"

He already did that wrong unless the Full Trad IRA (and related account(s)) never had any earnings.

"but he ends up taking and addition 4,000 on top of what he is calling a conversion so he has to me created more of a tax situation for her. she should be paying the penalty on the 4000 that was not converted plus tax."

Yes; plus withholding, if you see that.

"and I really have not been given the basis in her ira to figure it all."

At least you know enough to take that into consideration. Help her know how much he cost her and what an idiot he is, for his supposed profession.