Update! Here are some of my findings as to what happened earlier today that resulted in areas being randomly regenerated. I'm mostly posting this for anybody that is curious to know about what happened, regardless of the fact that these sort of things are typical and will occur from time to time with any early access games.
These are the two known regions that I was able to find, that was randomly regenerated: r.0.-5.7rg and r.3.1.7rg. Regions are large square areas of the world and each region is contained within a single data file. Upon visiting these areas, I was able to find that about 20% or less of these regions had been regenerated and resulted in a partial data loss of those regions. I also noticed that the portions that had become regenerated, also had lines going across them on the x and y axis on the map. I had noticed these lines appear before, but never knew what they were from until now.
These findings show that no foul play or any wrong doing had occurred, cause an entire region would have been regenerated instead, as opposed to only a small portion. Simply put, the region files had corrupt or incomplete data and resulted in a partial automatic regeneration of those regions. It is also most likely the result of merging the old content of Alpha 16.3 to the newer version of Alpha 16.4. By doing so, it had resulted in having random regeneration of areas with the newer version of Alpha 16.4. Regards.