Have you tried running the CLI script with you admin siteaccess' name as -s parameter ? Normally, one does not need to run this for every front siteaccess. Also, where are you having the URL issues from ? Back office or one of the frontend siteaccesses ?
which makes the code more portable, and much closer to eZ Publish standards.
Also please note that using .url_alias instead of .global_url_alias may be blocking in case you retrieve search results from other eZ Publish instances (3rd-party search with eZ Find). This is probably not the case for now, but should this happen in the future, come back to this thread and have another look at it.
Cheers !
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Nicolas Pastorino
Director Community - eZ
Member of the Community Project Board