Hello RemiD
I may not be the best person to answer your question, but, I’ll tell what I know
The files you mention are needed to upgrade the DSO203
SYS is the backbone of the DSO203.
APP communicates with SYS and gives the DSO its personality. So, different APPs you can find have different UIs.
CFG_FPGA.ADR and xxxFPGA.Bin are to be loaded in sequence (without powering off the dso) to the DSO203 as explained elsewhere on this site.
If you still have doubts remaining, ask here.
Easter greetings