Hello,
I would not recommend you re-flashing unless you have no other choice. Some of us already made that mistake and now have problems with restoring of their scopes systems. Unless you're very familiar with embedded Linux operating systems and you think you're able to restore such an OS. Thinking more about re-flashing, if a bad solder joint is causing the issue you will probably fail at erasing of the FLASH.
Boot log may stuck at "F" (FLASH) and still, issue may be caused by a faulty DRAM.
If you did check all supply voltage rails (Vrefs, DDR termination etc.) and clocks I advice you to check thoroughly bus traffic between CPU, FLASH and DRAM. Those scopes are pretty old and additionally if working hours counter in case of your scope is high (in my case - MSO4054 - it was around 27340 hours when a Micron DRAM failed) it may be something wrong with DRAM or any BGA IC solder joint. If in your case there are also Micron DRAMs installed I would say - suspect them first.
So, if I was you, I would download at least datasheets of: CPU, FLASH and DRAM and check all command/address and data lines.
So, warming up (a bit over) or cooling down (a bit under) room temperature and observe ICs using a thermal camera may also be helpful if you own one. If using a thermal camera, keep the scope powered on for maximum few seconds and make breaks because you don't want the power section of the board affect thermal imaging results (false negative). I confirmed several times that Micron DRAMs failures occur depending on their temperature (they usually work if warmed up and fail if cooled down).
It may not be easy, but if you really want to take up the challenge, then please remember ESD precautions like cotton clothes, anti-static gloves if you don't have access to EPA area where you could perform the repair.
Good luck.