Replacing 2 50 amp shore power with single 100 amp

I assume its a Viking SF? It depends on what electrical equipment is already installed in the E.R. . Mid 2000 Vikings have a Atlas auto former that both 50 amp inputs go to for phase polarity and boost and then a secondary backup shielded buck boost x-former if your Atlas PLC dies. Both of these units aboard are set up for two 50 amp inputs only. If you have the described Atlas than I don't think it'll accept one 100 amp input as its KVA isn't rated for that You would also have to remove the two existing cable masters and install one for the 100 amp cord and the 100 amp cable master is a beast size wise with the larger cable spool bucket etc. Seems to me that if your willing to remove the smaller x-formers and go with one larger 20 kva or so unit than it would be doable depending on your clients $$ pain threshold vs dragging two cable master assisted cords out. Personally I'd rather have the option of two fifties if I had to run critical services off of just one cord in an emergency.

What size boat? He s not going find many slips under say 80’ with 100amp service so he will have to carry the heavy and expensive 50 to 100 box...

Have you priced out 100A cords? 4 x 4AWG.
Heavy and expensive.
Most 50A cable masters can not be adapted for this cable.
Heavy expense to buy a 100A cable Master.

IMHO, cheaper and better to tip (well) the dock service to drag the light 50A cable if he can not do it himself.

First step is determining what isolation system that's aboard. If you have the Atlas in the aft Starb. corner of the E.R. and the secondary Acme x-former aft port. If your not equipped this way than maybe its a easier deal for you. I don't think that's its as strait fwd. as you believe by running a 100 amp svc into the exiting shore J -box and using the existing circuits / wiring from that point fwd. if you have this primary and secondary x-former isolation system. Does your J-box have a shore power contactor in it with auxiliary contacts for your secondary system Acme bump boost? The 2004 65 Viking I was involved with was optioned to the max from New Gretna and I believe the Atlas PLC controlled auto former was an option and an expensive one at that.

jdow,
I'm a glass half full type of guy and didn't mean to sound negative. I hope that you can achieve the desired outcome for your client . Outside of armchair marine engineers like myself , you need to consult a qualified marine electrician and preferably one who knows Vikings systems well.
So in theory yes, you can convert your two 50 amp cord system to one 100 amp. The only issue that comes to mind would be polarity on L-1 L-2 if you retained the split buss switchboard with one 100 amp service . Right now you have two 50 amp svc. feeding your main electrical switchboard that has a split buss arrangement. If you blow a shore breaker for one of the cords on the dock than you'll still have power on half of the switch board through the remaining energized cord. Each of your 50 amp cords will be going through a isolation transformer and have galvanic isolators on each along with circuit protection (Breakers) on the primary and secondary side of your isolation transformers. If this is the setup that you have than you would be required to remove the two small 10 kva isolation transformers and replace them with one x-former rated for 100 amps or 22 kva @ 240 volts and modify your switchboard for a single buss system or purchase a smart isolation transformer that has sensing taps for polarity. If you have the atlas setup with the Acme secondary isolation transformer than its going to be a bit more involved equipment removal and wiring wise. It shouldn't be more than a days labor rate for a qualified marine electrician to give you the correct answers for this scenario & it'll be $$ well spent .

As someone who has cruised extensively with 100' of 100 amp shore power cable on a cablemaster, I would rather deal with two 50 amp cords.