It was Microsoft/Azure bug which was fixed for us without any actions from our side (no deploys or any edits in Portal/CLI). I.e. after 2+ days logs just appeared in "Logs" page of Analytics Workspace (they even haven't been lost).
I can't see logs in Log Analytics Workspace instance from my contains apps since yesterday.
I have 3 Azure Container Apps connected to one Log Analytics Workspace and 1 Container App Jobs. Yesterday I've stopped to see logs from 2 of 3 these container apps. I see only logs from 1 app and job.
Those 2 container apps (by 1 replica each) where redeployed via Bicep without any other infra changes. Azure Portal for these apps shows full integration with Log Analytics Workspace even with "System" logs from them. But application's "Console" logs are empty.
One of these apps had "degraded replica" for couple of hours due to long db migrations and during this time, logs from new revision are available in Log Analytics Workspace, but once old revision pod was removed the logs disappeared as well.