What I have done in the past to force a download of all articles is to remove a couple of entries from the config file. In the "Pocket" section, remove the entry for "LastSync" and "UnsyncedUrls". The LastSync is probably the important one and as it stores when the Pocket sync was done last and only downloads articles added since then. Removing it should download eveything.
If you want to be a little tricky, the value for LastSync is an Epoch timestamp. If you know when the articles stopped downloading, then you can calculate the timestamp and use that instead.
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