From ModMyi - Wiki

As you've probably noticed, if you've sync your iPhone after installing free custom ringtones, iTunes will remove them. While some software, like iPhoneRingToneMaker, offers a single-click "restore my ringtones" button for use after syncing with iTunes, many of us still use the manual (and free!) iPhoneBrowser/SSH method. The single-click restore will also only work for custom ringtones installed from that specific computer. The following is a simple guide for the method I devised to "sync-proof" your free custom ringtones. -unclear

All you will need is the following software: Putty

Warning: This guide will most likely erase any and all ringtones legitimately purchased through iTunes.

Step One

Open putty.exe. Enter your iPhone's IP address. This can be found in the settings for the WiFi you are currently connected to on your iPhone. Hit enter or press the 'Open' button.

You might get a dialog with the heading WARNING - POTENTIAL SECURITY BREACH!! Don't worry, just hit the 'Yes' button.

Step Two

In the Putty terminal, login as root with whatever password you use (by default this is usually "alpine" or "dottie").

Enter the following commands:

cd /
ls

If you don't see iTunes_Control in the list, you have probably jailbroken your iPhone. If this is the case, issue the following commands (Do NOT do this if you already see iTunes_Control):

ln -s /private/var/root/Media/iTunes_Control /iTunes_Control
ls

When you see iTunes_Control in the list, with or without having to issue these commands, continue to Step Three.

Step Three

In the Putty terminal, issue the following commands:

mv /iTunes_Control/iTunes/Ringtones.plist /iTunes_Control/iTunes/Invincible.plist
ln -s /iTunes_Control/iTunes/Invincible.plist /iTunes_Control/iTunes/Ringtones.plist

What this does is copy your Ringtones.plist (which is erased by iTunes when synced) to a file called Invincible.plist. It then makes a 'shortcut' file to Invincible.plist called Ringtones.plist. This way, when your iPhone tries to open Ringtones.plist, it is linked to the correct file, but iTunes can't open it to erase its contents.

That's It!

To disconnect from your iPhone in Putty, issue the command:

exit

Feel free to sync away in iTunes, as it will no longer be able to edit your Ringtones.plist to disable any free custom ringtones. iTunes may give a couple errors about a file missing and the sync failing, just hit 'Ok' and iTunes will continue to sync anyway.

Troubleshooting

The following is for users that have completed this guide, but still lose custom ringtones after an iTunes sync.

The most common problem seems to be that many of you have jailbroken your iPhone, yet still have an iTunes_Control in your root directory. This would mislead you to skip step 2, and the mod would take no effect. iTunes would still be able to write the Ringtones.plist that is actually used (at /var/root/Media/iTunes_Control) as that file wouldn't have been modified to be 'invincible'. If this is the case for you, re-open Putty, login, and issue the following commands:

cd /
mv /private/var/root/Media/iTunes_Control/iTunes/Ringtones.plist /private/var/root/Media/iTunes_Control/iTunes/Invincible.plist
ln -s /private/var/root/Media/iTunes_Control/iTunes/Invincible.plist /private/var/root/Media/iTunes_Control/iTunes/Ringtones.plist
exit

Restart your iPhone for good luck, and you should now have "sync-proof" ringtones. If iTunes still manages to kill your custom ringtones, you must be on a different version, and you are probably out of luck for now.