It seems like you have two options:
- Remove the timeout in Apache.
- Delegate the chunk-combination effort to a separate thread, and return a response to the request as soon as possible.
With the latter approach, you will not be able to let Fine Uploader know if the chunk combination operation failed, but perhaps you can perform a few quick sanity checks before responding, such as determining if all chunks are accessible.
There's nothing Fine Uploader can do here, the issue is server side. After Fine Uploader sends the request, its job is done until your server responds.
As you mentioned, it may be reasonable to increase the chunk size or make other changes to speed up the chunk combination operation to lessen the chance of a timeout (if #1 or #2 above are not desirable).
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