I can't find anywhere in the manual on fuse size recommendations. Based on the specs I would assume a 200a inline mega fuse would protect the 200ah lithium battery (and cable--at 35mm2 with a 1m run), would this assumption be correct?
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Not really, as you have not advised what type of battery limits the Lithium battery has. and thus without all the information its not possible to advise you.
some only have a Max output of 80amps
anyway the fuse should be smaller than the maximum amperage output limit of the battery, and cable
https://www.victronenergy.com/batteries/lithium-battery-12-8v#downloads
You will find all the information here for the maximum current output of your battery here
There is no current limit with the batteries so it can produce whatever the battery pack can do (with lifepo4 it's a lot of amps). I wouldn't use a 200amp fuse with only 35mm2 wire even though that is a short run. I'd stick with a 125amp fuse or up your wire size depending on your loads.
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