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We need when updating to overwrite some existing files but it does not do it. We have only found the option available for the original files, not for the updates.
In the Existing article it mentions that:
Quick Patch Projects are great for delivering simple small updates, but they are limited in their functionality.
Unfortunatley they don't have access to the "always overwrite" setting.
Installshield Express does not have any other offerings to create patches which leaves 2 options:
1. Make sure that the files you want to include in the patch have a higher file version - this would ensure they are installed over the older files.
2. Create a full upgrade rather than a patch
Our Installshield Premier Edition has functionality to create a fully modifiable Minor Upgrade - and then using its "Patch Design" feature we can compare the new Minor upgrade against the previous version to create a patch.
The advantage of this method is that we have full access to all the project settings whilst creating the Minor Upgrade providing a greater level of freedom in what can be achieved.
Go to the files view - select your file > Right Click > Select Properties:
 
From the properties box that appears select the "Advanced" Tab - check the "Always Overwrite" and then select "Apply"
Hope this helps. 
Thank you for your reply, unfortunately this option is not available for new files in the Quickpatch project configuration which is what we need. I'll show you what we have as options. Even though we have "Install always", in some machines it won't overwrite the file.
If we right click on any of these files the menu we get has the options "Delete, Patch existing file, Insert new file", none of these are what we need.
Quick Patch Projects are great for delivering simple small updates, but they are limited in their functionality.
Unfortunatley they don't have access to the "always overwrite" setting.
Installshield Express does not have any other offerings to create patches which leaves 2 options:
1. Make sure that the files you want to include in the patch have a higher file version - this would ensure they are installed over the older files.
2. Create a full upgrade rather than a patch
Our Installshield Premier Edition has functionality to create a fully modifiable Minor Upgrade - and then using its "Patch Design" feature we can compare the new Minor upgrade against the previous version to create a patch.
The advantage of this method is that we have full access to all the project settings whilst creating the Minor Upgrade providing a greater level of freedom in what can be achieved.