How did you remove the silence? I can think of two methods;
- use iTunes' Start and Stop feature
- edit the file outside of iTunes
Each method has its own advantages and disadvantages.
iTunes' Start and Stop feature means that you can tell iTunes what time into the song it is to begin playing and/or at what time in the song to stop playing it. If you use this method, a Sync of your device (iPod, iPhone etc.) will add that change to the device*. If you have used this method and the song still isn't correct on the device, I suggest that you remove the song from the device as one Sync operation, disconnect the device, reconnect it and then Sync again to re-add it.
The simplest way to remove a song from your device is to untick the song (uncheck it) in your iTunes library. Providing the option to Sync only ticked (checked) songs and videos is still on, this will remove the song.
If you edit the file for a song outside of iTunes (for example, with an MP3 editor), iTunes will not realise that you have changed the file. However, I would expect that iTunes would then continue to use the unedited version, so your experience suggests that this is not the issue. That said, I think it might recognise the change if and when iTunes plays the song, but don't bank on it.
The advantage of using iTunes' Start and Stop feature is that it's easier and does not require knowledge of editing the file itself. The disadvantage is that the change is only known and recognised by your iTunes Library and any devices synchronised with it, or when you transfer your Library to a new computer (providing you copy the iTunes control file as well). If you move your song to another programme, your change will not be recognised.
The advantage of using an external MP3 editor is that then change is stored in the file itself and moves with the file. Therefore, if you move the song to another programme, the change goes with it. The disadvantage is that one needs a knowledge of editing files, it takes more work and is not recognised by iTunes until the song it played by iTunes Library's player (and even then, I wouldn't count on that last point).
* Although you stated that you use Sync, note that there is a crucial difference between Sync and Manually Manage. (I have noticed people on this forum use Manually Manage {or "manually sync"} when they mean Sync.) When using Manually Manage, you need to manually remove the older version of the song from the device, then add the newer version onto the device as a separate action. iTunes will not do it for you (whereas with a Sync, it will.)