I believe what you are saying is that the gain reflected on line 9(a) of your K-1 schedule is not all taxable, since some of it is excluded under section 1202. So, if you don't report the taxable amount on line 9(a), the IRS might assume you under reported your capital gain income.
The IRS does not allow for an entry on a form to reconcile the gain reported on the schedule K-1 and the taxable amount to report on your tax return. One would assume then that it is not unusual for the two to not agree, so it should not pose a problem.
This is similar to a situation where the cost basis on a form 1099-B (investment sales) is often not the actual amount of cost basis, so you have to adjust the amount on your tax return. This does not create a problem with the IRS since they are accustomed to the amounts not agreeing, and the forms do not allow for an explanation as to why.
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