There are multiple case scenarios, and they are mostly dependent on your iTunes settings. Both iTunes Library and FrostWire library work in similar ways. They both have their source folders where their actual files are stored and in addition, both can have files from outside of those folders indexed inside the Library. It all depends if you are deleting the files themselves or just their references from the Library and if iTunes has copied those files to it's Media folder or it only has indexed them before you decided to delete.
1. If your iTunes imported all files you've put in the iTunes library [Preferences or Options > Advanced > Checkbox by 'Copy files to iTunes Media Folder when adding to Library' ], then if you will delete the entire FrostWire Library and it's media files, your iTunes Library will not be affected, because it has it's own set of files it is already referencing.
2. If on the other hand, you were not copying the media files to your iTunes, but just referencing them (indexing), and you delete your FrostWire library and the media files, iTunes will still have the references of your downloads, but will not be able to play them, because the actual files won't be there. You will usually see an exclamation point next to the file iTunes can no longer locate a source for.
3. If you were not copying the media files to your iTunes, but just referencing them, and you delete your FrostWire library, but not the media files from the FrostWire Data Folder (or whatever was your default save folder), you iTunes will still have references of your downloads, and will be able to play them, because the actual source files are still at their original location.
Independently of your iTunes settings, each time you change something in your FrostWire library and you Rebuild you iTunes playlist from Tools > 'Rebuild iTunes 'FrostWire' Playlist', the 'FrostWire' Playlist will be synced to your FrostWire Library. Files that were copied to iTunes Media Folder will not be removed from the overall iTunes library though.