Reformatting hard drive question reguarding JJOS

I have an MPC2500 with JJOS1,JJOS2, and JJOSXL installed. I have some folders on my hard drive that I cannot delete. Invalid syntax error, whole bunch of crazy symbols, and nonsense. So my question is, if I reformat the hard drive from the MPC2500, will I still retain the JJOS's? Basically what I'm wanting to know is once the hard drive is reformated and I dump my projects back onto the MPC, will I be good to go, or is there other steps that need to be done? Nothing is wrong with my CF card, and all the bin files are stored on the CF Card. Am I overlooking anything? Please offer some advice. Thanks.

Yes, all good man. Just did this last week. But make sure to reformat in either the free JJ OS or JJ OS 1 ONLY.

http://www7a.biglobe.ne.jp/~mpc1000/mpc ... ortant.htm

Oh I forgot to mention the obvious...BACK up your drive first!