I had this happen before and it was due to a failing hard drive (SSD drive that needed cooling, was overheating and corrupting files). I was able to fix by 1st fixing my cooling issue by adding a heatsink to my SSD (or replace the failing drive - hope you have backups!!), then restoring the world 'parts' DBs that were corrupted (a 'world part' makes up many chunks) and is in the "worldParts" folder.
#1 - you need a recent backup of not just your world DB, but your entire worldParts folder (backup your entire server folder daily or at least weekly - archive monthly backups).
#2 - Identify which world part DB is corrupted. Go to the problem area in game and press F3. On this big hud menu, it will tell you which world part you are in. Take careful note which world part you are in, could be for example "wp0_-11.db" or "wp0_11.db" (11 without the minus). Undeveloped worldpart DBs are 20k in size, will be larger than 20k if that area has been constructed upon. Compare the wp0 (world part DBs from latest backup with those in server folder). I found that if the DB becomes corrupted, it reverts that entire world part and anything within it back to default SEED (so if backup reads that world part as 1,512kb in size and your server folder shows the same db as 20kb, it got restored to seed, thus deleting all modifications within it back to the way it was when 1st created). A building can be in 2 world parts (at the border of world parts) which would result in half the structure being shaved away.
#3 - once you identify which world part has been affected, restore it from your most recent backup.
#4 - i believe a chunk is only 12x12 or 24x24 block in size. A world part is much larger than that, (the more developed a world 'part', the more chunks it contains). I had several claims affected and traced the border of the world part and was approx 12x12 map grid squares (or larger), and any loss of parts of buildings. You may want to look around a huge area to see if you lost other buildings/claims etc. Claims that crossed worldpart borders, looked like they were cut in half (half build, half nature).
In my case, I found 2 world part DBs in the 'worldparts' folder that were corrupted, which affected many builds. If I refreshed the map in those areas, i noticed all modifications got refreshed out, back to nature. I then marked the world part boundary on my map and could see I lost a lot of builds, until I restored them from backup. I used F3 in game HUD menu to identify where world parts ended and others started while riding horse, then marked them on my map and checked nearby builds within the corrupted world parts. fun fun
I hope this helps and that you have backups!!
Good luck