DOMDocument.xml Refreshing

In general, it turned out that I had to delete almost a thousand symbols manually by opening fla as a zip, and now when opening a fla file, I still have those symbols in the library that I deleted, but they are empty. In general, all this is due to the fact that DOMDocument.xml still thinks that these symbols exist, so is there any way to "update" DOMDocument.xml not manually? For example, using jsfl or python script?