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Not the easiest but if you were to use repair care you can drop a piece of perspex in the groove and build the edges up to it. It won't stick to perspex so you get a decent finish. otherwise just build it up by hand and chisel the edges of the groove. There are other methods. I had to do one recently, turned out fine.
You could cut the existing cill out and replace it using repaircare to fix the joints. I do that occasionally but it's kind of preferable not to cut them out because you have to cut through the mortising, sometimes it's necessary.
The way you are doing it will be a bit of a bodge because your door opens inwards, the rubber flap on the stormguard would be more effective if it closed onto something, having to close over the edge of the cill means it will be likely to have a gap under it so there will be a draft. In this case it's better to have rubber strip on the back of the door that provides some sealing. That is if you decide to delete the water bar.
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Airhead
Howard
The existing water bar has failed somewhat catastrophically; where it's fixed in to the cill it's let water in to the fabric of the wood and it's all rotting. I'm not sure it would even be possible to fit a new one reliably.