Sorry about taking so long to reply, things kinda got busy. I was able to get some testing done on Ubuntu and found that the recipes will keep the correct levels in single player mode. Seems like there is a bug somewhere between the client and host. seems like when the server is shut down it defaults all the recipes back to level 1 with 6400 needed to level them up, if anyone could reproduce this would help.
(the steps I took to get here are as fallows. First I made a new server, then start the server to create the default server.cfg, then I shut down the server and edit the server.cfg, and I change the "RECIPE_LEVEL_AMOUNT" from the default 4000 to 1000 then save the newly edited sfg, and I start the game and reset the universe and clear the client cache. I then start the server, and a new client, buy a recipe of some black hull and white hull both saying 0 blocks needed to level them up but when I start to make blocks from the black hull recipe it changes from 0 to 1600. I level the black hull recipe to level 2 and then close the game client. and then restart the server, when I relaunch the game client and start the game I find that the black hull recipe has reset to level 1 and needing 6400 to level it up, now the white hull will change from 0 needed to lvl the recipe to 1600, but when I put the white hull recipe in factory it changes from 1600 to 6400 needed to level up.)
Once again, sorry for taking to long to reply.
PS: I have attached my server.cfg to this post.