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I generated pdf files of the tax returns (for filing) with and without safe harbor election and compared them page by page. There are two differences:

1. The safe harbor statement does not exist for one of them as expected.

2.  In the tax return with the safe harbor statement the 8995-A form does not have part 1c (check if aggregation) box checked. As a result there is no Form 8995-A schedule B (Aggregation of Business Operations) in this tax return.

I don't know whether item 2 is a bug in TT or whether it is intentional since the list of properties also appears in the safe harbor statement (in a slightly different format than in 8995-A schedule B). While entering data, I clearly elected to aggregate all properties for both tax returns. 

 

Since  it doesn't look like TT will fix the e-filing issue anytime soon, I am considering the following options, if the presence of the 8995-A schedule B form in the return is not a problem when electing safe harbor (why should it be a problem since the aggregation is intentional)

a. E-file without the safe harbor election but mail the safe harbor statement to IRS separately through registered mail. IRS does not see the steps the user goes through to get to the final tax return. They just see the result. The only thing missing during e-filing will be the safe harbor statement which IRS will receive through regular mail. The e-file will include a 8995-A schedule B form that lists the properties in the aggregation.

b. Same as option a but without mailing the safe harbor form to IRS. Instead just sign and date the safe harbor statement and keep it for the record in case of an audit.

c. Same as option b but get the safe harbor statement signature notarized for future use in case of an audit.

 

Thoughts?