Perhaps "It will all come right in the end" is British usage.
In the US, you may hear any of the following:
It will be all right in the end.
It will come out right in the end.
It will come out all right in the end.
It will turn out all right in the end.
You can substitute "It'll" for "It will."
You can add an optional "all" as in "It will all" for any of these.
To be "all right" it just means that the situation is okay, under control, no lasting damage, etc.