So have you gotten two 1099-R forms? Or are you saying that the old and new providers somehow coordinated in sending you one form?
If you got two forms, the one with the total distribution needs to be corrected. The instructions for the 1099-R (page 12) state
"Box 2b. Total Distribution Enter an “X” in this box only if the payment shown in box 1 is a total distribution. A total distribution is one or more distributions within 1 tax year in which the entire balance of the account is distributed."
That is, a distribution to the taxpayer. Changing administrators is more like a rollover. Most pension administrators don't even issue a 1099-R for a rollover, because there is no tax consequence to you.
So, your first impulse is right, contact the pension administrator who issued the 1099-R with the Total Distribution checked and ask them to rescind it. Otherwise the IRS will be looking for you to declare both 1099-R forms.
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