I have added a notification webhook to integrate with other software on order creation. This works for a short time period, then I check back to Shopify, and the webhook has been removed. I've tested and demonstrated this atleast 5 times, and I don't know why this keeps being removed.
I should add, I've tried going through Shopify support who keep insisting I post here, although - it's quite clearly a shopify bug. I'm making it known in a public forum that i'm totally unimpressed in the support provided by Shopify.
It's hard to say exactly what's going on with your experience without knowing more information however in general, webhook subscriptions will be removed in these cases
you delete the subscription (in the admin for merchant webhooks or through the api for an app webhook subscription)
you make a change to the app scopes and the app no longer has the required scope for the topic you had a subscription to (ex: read_orders gets removed from the app config then you'll no longer be able to get orders/create webhooks)