I would break the larger sequence into chapters, export the chapters (self-contained or reference) as a batch, then do the encode in compressor as a batch.
This way, each block is independently playable. You are not dependent on ALL the blocks coming through unscathed and being successfully relinked before you can see ANYTHING.
If this is something you will regularly do, you might be able to automate most of the process. For example, you could set up a watched folder that will be the FCP export target. When a file shows up, Compressor starts and encodes it and puts the outcome in a second folder. That folder is set up to FTP anything that shows up in it to your client's site. It may take some time and effort to set up the process but once it is in place, it is something that can run unattended overnight.
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