class.upload.php is a powerful and mature PHP class to manage uploaded files, and manipulate images in many ways. The script is available under a GPL license.
I don't understand fully what you want to do. So you have some images (large and thumbnail) already on the disk, and you want to process them locally.
Then you want to process them both, applying some transformation one both of them, or only one? And it works only when it applies the effects on both of them?
You say that you need to have $handle->process to be true. That is not strictly correct. You need to call $handle->process() twice, once for each image. In between each call to process(), don't forget that all the parameters are reset.
Then you want to process them both, applying some transformation one both of them, or only one? And it works only when it applies the effects on both of them?
You say that you need to have $handle->process to be true. That is not strictly correct. You need to call $handle->process() twice, once for each image. In between each call to process(), don't forget that all the parameters are reset.
Could you paste here your log(s)?