Thank you for getting back to me.
If you are not using external templates for the Images and Documents back-end controls, then you should not worry about forgetting files. If however you use them you should merge yours with the external templates for your current version of Sitefinity. However I doubt that this issue is coming from this. I have replied to your support ticket with similar issue. As I noted there this might be IIS caching your files in memory. You can try with application pool recycle to verify if this is the cause.
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