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You can definitely call both of them from a Host VI, you just need to call the Open FPGA VI Reference on each of your targets. For an example of what this looks like, check out the Peer to Peer example which shows how to stream data directly between two FlexRIO FPGA Modules. You can find it in the Example Finder, under Hardware Input and Output > FlexRIO > Peer to Peer.
As you mentioend I can use the Open FPGA VI Ref to get reference to each target. This is for example 1 of my VIs.
Inside these subVIs I use FPGA Read and write controls. Can I copy and paste the same blocks in my top VI and pass teh second FPGA ref or I haev to pass teh second FPGA Ref and modify the subVIs as well.
2 Tragets are completely sperated and I don't need to worry about timing stuff between them