why would you want to or need to modify the standard deduction?

Standard deduction should be modify when tax payer, a Puerto Rico resident,  excludes income earned in the territory. For example, if taxpayer has $90 in income earned in the mainland and $10 in income earned in the territory-- as a Puerto Rico resident, taxpayer can exclude $10 from Form 1040 but should reduced the standard deduction by 10%. 

You may want to edit the title of your post to include something about Puerto Rico, so that someone familiar with it can respond, I have no clue how this works, sorry.

Have you tried just overriding it?

Then when you e-file from Homebase, disable error-checking.