Magento: all products suddenly cease to be in stock after re-indexing

I have a Magento site with about 500 products, and a couple of times in the last year I saw how they suddenly and inexplicably disappeared. I believe that this happened immediately after we redefined some indexes (from the shell).

I run the full re-indexing procedure, and the stock returns to normal.

But for the site there is still a period of "downtime", which is undesirable.

Can someone explain why this can happen, and what can I do to avoid this? Also, how often should I reindex, ideally?

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We update the indexer.php index in the shell folder with cronjob at 3 a.m. without changes to the database. If we change items / categories. etc. we will index right after all changes.

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