FWIW, I run all my old machines on CF->cheap IDE adapter->R-IDSC-E SCSI setup. Normally, this is a great setup.
However, on my development IIx where I frequently hang, crash, or otherwise just have to power cycle the machine, I started getting problems saving my source files, which I commonly had open, probably during most of these reboots. Booting from a disk tools floppy and repairing the volume resolves the issue for me until a few more power cycles go by. But keep in mind repairs like that are on filesystem metadata, not on the data stored in the filesystem. In my case, some chunks of data were lost from my source files, but if the data were lost or corrupted from an app you're running or something, you may have worse results. I don't believe this is specific to flash media, although it may be exacerbated by certain characteristics of CF cards or the SCSI->IDE command translation. The moral of the story for me is not to do development on the test machine.
However, on my development IIx where I frequently hang, crash, or otherwise just have to power cycle the machine, I started getting problems saving my source files, which I commonly had open, probably during most of these reboots. Booting from a disk tools floppy and repairing the volume resolves the issue for me until a few more power cycles go by. But keep in mind repairs like that are on filesystem metadata, not on the data stored in the filesystem. In my case, some chunks of data were lost from my source files, but if the data were lost or corrupted from an app you're running or something, you may have worse results. I don't believe this is specific to flash media, although it may be exacerbated by certain characteristics of CF cards or the SCSI->IDE command translation. The moral of the story for me is not to do development on the test machine.