`theme deploy` seems to reset `content_for_index`

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Whenever I do a `theme deploy` the settings on my store homepage seem to be reset. Is this normal?


I've bought and customised the Blockshop theme and configured a Featured Collection section on the homepage. I note the homepage (index.liquid) is little more than

{{ content_for_index }}

which from Googling seems about right.


I've made some tweaks elsewhere in the theme code and then run a `theme deploy` and the collection assigned to this Featured Collection section is removed.  Coming from a CMS development background this seems wrong, but I'm wondering if that's just the way Shopify works or if I'm doing something wrong?