Here is the Help article for ProSeries and 1099-R:

https://proconnect.intuit.com/community/individual/help/proseries-form-1099-r-faq-s/00/4853

You simply enter that into the worksheet, marking whatever applies, and fill in amounts.

"BUT THEY CAN AVOID THE TAXES BY ROLLING IT OVER ALL OR PART OF IT TO AN IRA ACCOUNT BY THE DUE DATE FOR FILING TAX RETURN"

Are you confusing "deemed distribution" with "loan offset?" One means it wasn't repaid. The other is, it is Reducing a payout. An offset is allowed to be repaid; as an example, you borrowed $1,000 and have $5,000 in your account. When you quit, they only give you $4,000 as a rollover; you have to provide that missing $1,000 for the rollover to be "made whole."

Loan repayments are not considered to be contributions. You would not have a contribution as well as the loan repayment unless More than the loan was paid into the IRA. If that happened, the amount that has nothing to do with the borrowed amount also has nothing to do with the 1099-R. It's the new contribution amount, and no form would be issued for it until later. The Form 5498 is issued for money Into an account; that isn't a tax form; it's Informational. That's why you can't find anywhere to enter it. Only the 1099-R matters, and then you checkmark any action(s) taken. And that might be more than one thing.

Every little thing you asked depends on every little thing that happened. Just work through the client's details.