Unfortunately most of the time that I made my mod the file was not set to active, but it saved fine. Also, some of the pieces that are still there were made when the file was not "active"
You will forgive me, I hope, but this isn't possible. Changes are
only saved to the
active plugin in the CS. Perhaps you saved those changes in a different plugin that you are also loading, or perhaps your plugin was actually active; but in any case, nothing you have done has been saved to a plugin that was not active at the time.
Here is what you need to do.
Open the CS with all the plugins you want loaded. Make the one you want to edit the active plugin.
If you want to use objects from other plugins, follow these steps:
1) Double-click the object from the the object list to edit it.
2) Give it a new Editor ID that is unique to you and your mod. Click "OK".
3) When asked if you want to create a new form, click "Yes".
Now use YOUR version of the object in your plugin, and the changes will stick when you save. Placed objects originating from other plugins will vanish when you save.
Unfortunately, there is no way to "fix" your plugin except by re-doing it, because the data is gone.
Hope this helps, anyway.