When importing multiple files into your PLC project, TwinCAT 'Import from ZIP' feature will add the files and rename them as default if some of the files already exist in your project. This might cause some confusions and errors. You can change the option to Overwrite objects in the options menu if you need to overwrite the files in the project.  

Importing with default settings: 

Right click your plc project and select import from zip. 

As default, add option is selected. 

When you proceed with this option, you will have duplicate files in your project if the files you are importing already exist in the project. 

Changing the import/export settings to Overwrite option

We can change the import/export settings in the options menu. Click on Tools and select Options. 

Find the TwinCAT on the left menu and expand it. Select 'Zip export/import'. On the right menu, change the Import Action setting to 'Overwrite object and add if not exists' and click OK.

After this change, AddOverwrite option will be selected automatically in the Zip Import Dialog window.