I'm asking this because I did not find any updated tutorials and I tried myself but I think that I messed up with something...
I know that each plugin may create a data file, so I'm talking about wiping a vanilla server basically.

For example, if I wanted to delete everything, I would need to go to server/server_identity/ and delete everything besides the folder "cfg", am I right? I did that and my server broke, my plugins stopped working and I'm having a difficult time to fix that.
On the other hand, if I wanted to wipe only the map, I would need to delete the two files ending with .map and .sav, correct? 

I really think that a tutorial on that is missing for beginners like me. Thanks in advance for the patience and help!
Have a good day!

For basic vanilla wipe you delete the 2 map files .map and .save
Also if you want to wipe blueprints delete the player blueprints file.

For plugin wipes depends on which you are using. Backpacks for example you delete the backpack data files. If not then players with items in their backpacks will still have the items after map wipe.

Same if you use kits and have one for example a wipe kit that can only be used once. You will need to delete the data file that holds the player info so that it also resets their use count.