You can't buy a ticket that is valid on the "classic" lines one way, and on HS1 on the return, from any machine or online.
The way that a journey like this should be made, without overpaying, is to buy the ordinary "not via HS1" ticket and then to obtain either change-of-route excess (to "Plus High Speed"), or a HS1 upgrade ticket.
It is perfectly permissible to obtain the excess or upgrade onboard the train - without penalty - but if you wish, you can obtain the excess at a ticket office (or earlier train) before getting on the HS1 train.
The cost of the excess, for one portion of a return, is half the difference between the appropriate return fares. For example, if you had an Off-Peak Return from London Terminals to Gillingham,
route 'not via HS1', which costs £28.00 without a Railcard, you'd excess that to the Off-Peak Return,
route 'Plus High Speed', costing £31.90. The difference is £3.90, thus you'd pay £1.95.
The difference payable will vary depending on the exact ticket you hold - e.g. for an Off-Peak Day Return it would be £2.05, for an Anytime Day Return it would be £2.95, for a (Weekend) Super Off-Peak Day Return it would be £2.00, and for a Weekender ticket it would also be £2.00.
Of course, if you travel during a time where the ticket isn't valid (e.g. on an Off-Peak Day Return before 09:30) then the difference would be to the appropriate ticket, as valid at the time of travel. That may be more, or less, than I've indicated above.
The HS1 upgrade ticket costs more than any of the above amounts, therefore ask for a change of route excess as opposed to the separate "upgrade" ticket. If you're sold the more expensive "upgrade" ticket then pay it at the time (if the member of staff insists), but contact Southeastern afterwards to recover the difference.
