i think you may be misapplying the rule for suspending the use test. for up to 10 years you can suspend the five- year test period for ownership and use. (IRC 121(d)(9) and (12)). This election is available for any period that you are on qualified official extended duty QOED). QOED is any period you are called or ordered to active duty for more than 90 days (including an indefinite period) you must also 1) be serving at a duty station that is at leat 50 miles from your main home OR 2) residing in government quarters under government orders. there are also rules for who is eligible.
it seems you're saying you have lived in that property which you owned for the entire period. in this case the regular rules for home sale exclusion apply. if you own the property and live in 1 unit as your principal residence meeting the ownership and use tests, the HSE only applies to your unit only. Upon sale of the property the other units would be treated like a vacation home - not eligible for the exclusion. As rentals depreciation allowed or allowable on the other two units would be subject to recapture. I have no advice on how the HSE exclusion would apply if during the 5 years you before sale you lived in different units as your principal residence.
allocation of sales proceeds would be based on the relative Fair Value of the units. you may want to use a pro to get a valuation.
