Sched C was disallowed but it was because deductions were applied to wrong income source

If the IRS has already corrected your return there is no need to also amend it ... but if you want to make the corrections for your records then use the amendment process just don't mail it in unless you need the IRS to reconsider something.  

Be careful ... the amendment process must start with the return AS CORRECTED by the IRS ... column A must reflect those amounts if you are going to file the 1040X.

See this TurboTax support FAQ for how to amend a tax return originally completed and filed using TurboTax - https://ttlc.intuit.com/community/amending/help/how-to-amend-change-or-correct-a-return-you-already-...

You can always amend.

You file a corrected schedule C with an explanation on Form1040-X.

If your calculations are correct and your explanation makes sense, IRS will approve it.