Yes, you can map flash to RAM and access the SRAM. See the Developer's Guide (
http://www.frank-buss.de/kerberos/developers-guide.pdf ) how to access the SRAM, page 3 (regs are here:
https://github.com/FrankBuss/kerberos/blob/master/c64/src/regs.inc ) and page 7. If you load a program over MIDI, it is saved in $10000-$1ffff in the SRAM, so the easiest way would be to load your program with the samples once, then you can load the program only and read the last loaded samples from SRAM.
For mapping the flash to RAM, you can enable the game cartridge mode, which allows to map any flash area to $8000-$9fff as ROM (maybe I should make this available for the menu as well, because then 4 k CRT files could be saved in the slots and then used). In fact that's the way the menu loads a program from a slot in flash, see
https://github.com/FrankBuss/kerberos/blob/master/c64/src/main_menu.c#L155 . So you could store your samples as a program in a slot, or even 1 MB as an EasyFlash image, then access it from your program with this method.
If you start the Kerberos App with the command line argument "debugging", you can even load the entire flash with the "Dump flash" command from the "MIDI config and test" tab. Then replace maybe the second 1 MB with your samples and save it back with "Upload flash". But be careful with this function, you can erase the menu with it, which is at the beginning. But if you have a SD2IEC drive, you can always restore it by loading the menu from
https://github.com/FrankBuss/kerberos/raw/master/c64/menu.prg on the C64 and then flashing
https://github.com/FrankBuss/kerberos/raw/master/c64/menu.bin with the "Flash menu BIN" function on the "File transfer" page in the Kerberos App again.