If you check this field, the software uses the corrosion allowance as it always has when computing the final stresses on the flange. If you say no, when the stresses are computed, the corrosion is not subtracted from the flange thickness. Saying no here will typically produce a thinner flange that is not as highly stressed. Also the MAWP of the flange will usually be slightly higher.
Since this is not directly addressed by any code, agreement on this subject is usually between the client and the manufacturer.
The flange thickness is used in several places throughout Appendix 2. The Code states
that every dimension used should be corroded. In the flange stress calculations the
flange thickness is used. However, some feel that the corrosion should not be taken
off of the thickness for the stress calculations.