iCloud Music has deleted my music files from my PC hard drive

I recently turned on iCloud music and synced my iPhone to iTunes on my PC. I noticed that Icloud music was uploading quite a large amount of my music files and thought that this was not right. I stopped the upload and turned off iCloud, only to find that hundreds of my music files on my PC hard drive are now gone! I tried to go back into iCloud music to see if I could download my missing files but the only ones it will let me download are the ones I still have on my hard drive ***?? All other songs that I want to recover are all grayed out in iTunes. I have run out of options and literally tried everything. Not happy that iCloud can remove files from your PC without you knowing. I know this has probably come up recently here...but can someone from Apple please help. Thanks.