and doing all the serial communication
at 2.5V (for reasons to do with being very space constrained).
Quoteand doing all the serial communicationSerial communication with what? Not the SD card. That doesn't use serial communication.
Quoteat 2.5V (for reasons to do with being very space constrained).How? Arduinos are typically 5V devices.
I've never wrecked a SD card powering it the usual way. That you have, powering it in an unusual way, struck me as somehow relevant.