In the case of Aluminum alloy, is it a common phenomenon to lose EBSD solution % significantly, when the same location is used many times? Does the electron bombarded region lose phase index after a certain number of runs? is there any method to recover the same location without damaging the microstructure and run EBSD again?
It can happen to any EBSD investigated sample.
It is called carbon contamination, here is whole discussion about it:
https://www.researchgate.net/post/How_do_you_prevent_disturbing_contamination_in_SEM_during_long-time_investigatons_like_EBSD_scans
You can recover the area by ion polishing with Ar ions. Other techniques like repolishing will always make changes to the scanned area. It is easier probably to reduce the carbon contamination than remove it later after each scan.
Another possibility is sample degradation due to beam damage but it is not the case Aluminum alloys.