How can playlists be preserved in iTunes?
The best way to preserve your playlists is to manage them, as far as possible, within iTunes.

It seems to me from your question and comment that the biggest issue arises when you rename a file you've previously added to a playlist. However, instead of renaming the file within your operating system, you should do it within iTunes. One way to do this is:


Within iTunes right-click on the song
From the context menu that appears, select Get Info (or Info)
This brings up all of the metadata for the song, including the field for its name
Rename the song
Click OK


Managing all of this via iTunes will ensure you don't break your playlists.

Also, you may want to check your advanced settings within iTunes and play with the Keep iTunes Media folder organized and Copy files to the iTunes Media folder when adding to library options to determine what works best for you.