The regulations for both 195 and 709 are almost verbatim as copied below:
A partnership is deemed to have made an election under section 709(b) to amortize organizational expenses as defined in section 709(b)(3) and §1.709-2(a) for the taxable year in which the partnership begins business. A partnership may choose to forgo the deemed election by affirmatively electing to capitalize its organizational expenses on a timely filed Federal income tax return (including extensions) for the taxable year in which the partnership begins business.
Based on the above, the election is deemed to occur by just expensing the item. If something is reclassified as organizational instead of operating, then so be it. Just a reclassification. It was still expensed. If the amount exceeds $5,000 then where you would be impacted is that all of the amount will not be able to be expensed in the year of adjustment; this is regardless of whether or not you would have made a "protective election".
Practitioners handle this differently depending on their practice. Based on your comments, it would do no good to only have these "protective elections" in your file copy but not with the return that is filed with the IRS.
*A reminder that posts in a forum such as this do not constitute tax advice.
Also keep in mind the date of replies, as tax law changes.
