Your crawled website pages have disappeared from your content library after you connected a store. This is expected behaviour on the free plan, and this article explains it so you know what you are looking at.
What happened
The free plan holds one content source. When you connect a store, the store takes that place and your website crawl is removed to make room.
Removed means deleted. The crawled pages are gone from your library, and they are gone from your agent knowledge. There is no archive, no trash, and no restore.
It happens without a confirmation beforehand and without a notification afterwards, which is why the usual first sign is simply noticing your Websites section is empty.
It removes every crawl, not just one
If you had crawled more than one website, all of them are removed, not only the one matching your store domain.
This matters most if you were previously on a paid plan with several websites crawled and then moved to the free plan. Those crawls survive the downgrade, but the next store connection clears all of them.
How to keep your website content
Upgrade before you connect the store. On a paid plan there is no single source limit, so your website crawl and your store coexist and nothing is removed.
If you have already lost the pages, upgrading and crawling the site again is the way back. Note that on the free plan you cannot re-crawl while a store holds the slot, so upgrading is required either way.
Do you actually need both?
Before upgrading purely to keep both, it is worth asking whether you do. Your store already supplies product information, and store pages often duplicate what a crawl picked up.
Website crawls earn their place when your site has content the store does not: shipping policies, returns, sizing guides, about pages. If your crawl was mostly product pages, losing it may cost you very little.
Frequently asked questions
Can support restore my pages?
No. The removal is permanent, so re-crawling is the only route back.
Does this happen on paid plans?
No. Paid plans keep both.
I installed from the store app marketplace and was never warned.
Correct, no warning is shown on that path either. The behaviour is the same.