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That's great about our setups being similar. I've had the SKR & 2209's working just fine for a while, and also use Octoprint for my terminal. I've had two printers for a while, and am about to set up a 3rd & 4th (after finishing my AKLP rebuild). Managing all those without Octoprint would be cumbersome.

The most important habit I have learned with compiling and flashing firmware, is to M502/M500 twice with every reflash. This obviously wipes your Delta Calibration and ABL, so I don't bother with the full probe routines again until I've fine tuned configuration.h for whatever #define I'm adjusting. I did allot of recompiling and reflashing last weekend to dial in my DELTA_SMOOTH_ROD_OFFSET, and that was my solution for getting frequent and fine the adjustments to take hold.

Also, I was able to get reliable EEPROM storage by commenting #define PRINTCOUNTER (line 1797 in your conf). Disabling that prevents marlin from storing print statistics over your level mesh and such. I know you are using SD Card settings at this point, but that is another way of solving the problem of corrupt EEPROM.