It looks like all the files that get indexed are not code files, but built objects.
16:26:45.889 INFO Base dir: C:\01.WorkSpace\03.Cyber\JTOSDPREADERSEC\09 Static_Code_Analysis\Code\MCU_CODE\U8.2\Template\Keil_project
And the actual code files might be somewhere else:
16:27:00.961 WARN File 'C:\01.WorkSpace\03.Cyber\JTOSDPREADERSEC\09 Static_Code_Analysis\Code\MCU_CODE\U8.2\Firmware\GD32F30x_usbd_library\device\Include\usb_ch9_std.h' is ignored. It is not located in project basedir 'C:\01.WorkSpace\03.Cyber\JTOSDPREADERSEC\09 Static_Code_Analysis\Code\MCU_CODE\U8.2\Template\Keil_project'.
I suggest reevaluating what directory you’re starting the sonar-scanner from, and reevaluating your -D"sonar.sources=../../" configuration (instead of backtracking through the directories, just remove this configuration and execute sonar-scanner from the directory your code sits)
I’ve also gone ahead and hidden the post where you shared the scanner logs. Please make sure you redact tokens (and consider the one in the logs you shared compromised).