When I download program into FLASH memory for FLASH programming I can see differences between my *.elf and *.hex File.

Normally the download patterns are the same for *.elf and *.hex file. Under some circumstances it is necessary to patch the *.hex file with additional patterns that do not exist inside the *.elf file. UDE implements a special Hex/Elf option to support that cases. The download pattern are taken from *.hex and the symbol information is taken from the *.elf file.

The option could be found via menu Config - Debug Server Configuration - Symbol - Hex/ELF load.