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A few things ...
1. The only way for a plugin to get access to a file inside of Sigil is via the plugin interface calls. Please make sure you are using those as demonstrated in the sample plugins
2. Make sure your plugin run() method is properly returning success upon completion (0) otherwise any changes made by your code will be aborted inside of Sigil (it will look like nothing happened).
3. Make sure if any exceptions happen they are caught properly and run() returns properly
(see point 2 above).
4. Please understand, you are not working directly with files inside of Sigil or the epub. You are interfacing using a copy on change style model where the changed copies are not updated inside Sigil until the plugin has returned successfully with a return code of 0 and the new files are all parseable.
Hope this helps, if not you can privately post your plugin code someplace and pm me (KevinH) or DiapDealer with the link and I would be happy to track down and fix any issues in your code or ours when I get home from work tonight.
KevinH
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