> I have to do a border run
Even if you have made two valid E-Visa applications, you need to do a border run anyway. Just having another E-Visa doesn't extend your stay or change the "Permitted to remain until.." date in your passport.
But if you applied for an E-Visa for your initial arrival in Vietnam, then applied for one with a later date to 'extend' your stay, there's a fair chance that the E-Visa you expect to use to fly to Vietnam may be invalid.
Airlines can check the validity of E-Visas: https://evisa.xuatnhapcanh.gov.vn/en_US//web/guest/hang-van-tai
If you did it that way round, you're running the risk that the airline won't let you fly or that you'll be denied entry to Vietnam (and made to fly back home or pay lots of $s to sort it out at a time when you're out of other options).
If you did it the other way round, all you risk is getting stuck in Cambodia or wherever until you can get another E-Visa to come back to Vietnam. (Of course, that isn't risk free if you're cutting it fine for getting back to Vietnam for a flight home.)