Im a complete noob, so my language wont be technical
One of the examples has a section where by it only writes to the SD card periodically. it buffers the data inbetween onboard the arduino. This is used because it uses a lot of a battery power to write to the card. on the flip side if the power dies you loose what was saved to the buffer in that period.
perhaps you could use that function, make the writes to SD card occur only once every half hour or so? (or even on the half hour using the RTC, so you know how much time you have to take the card out and do what you need to do?)
also, my SD card breakout board has a pin which can be used to tell when there is a card in the slot (or not)
you could use that function so that when the card is missing, the sketch buffers the data. once the card is returned to the slot, it dumps what it has saved and carries on as normal
I have NO idea what the removal of the card does to the sketch.