The following may be the problem:
Correct syntax should be: hwupload_cuda=1
It is in fact possible to use multiple GPUs from a single FFmpeg command line. There doesn't seem to be a lot of information out there on this topic. However, the following example uses GPU0 to perform resolution-scaling, then GPU1 and GPU2 to encode different formats (1080p, 720p).
In FFmpeg command line, assigning each NVENC encoder "-gpu 1" or "-gpu 2" is completely pointless, as the encoder always uses whatever GPU was targeted by the previous hwupload_cuda command, regardless of NVENC GPU preference in the command line. If you (nonsensically) specify separate GPUs for Upload and Encode, the Upload GPU setting overrides the Encode GPU setting, and both actions take place on the Upload GPU. So adding/removing the NVENC "-gpu" options makes no difference in function.
Using 3 GPUs is hilariously inefficient for such a small job, but the following command is a working example of FFmpeg running a complex operation using 3 GPUs at once. Using uncompressed AVI file input, which seems the most similar to what VoPro is doing (no hardware decoding):
ffmpeg -y -probesize 42M -analyzeduration 10 -i "d:\temp\input.avi" -filter_complex:a "[0:a]asplit [asplit1][asplit2]" -filter_complex:v "[0:v]hwupload_cuda=0, split [split1][split2], [split1]scale_cuda=1920:1080:interp_algo=4:format=yuv420p:force_original_aspect_ratio=1, hwdownload, hwupload_cuda=1 [split1scaled],[split2]scale_cuda=1280:720:interp_algo=4:format=yuv420p:force_original_aspect_ratio=1, hwdownload, hwupload_cuda=2 [split2scaled]" -map "[asplit1]" -c:a ac3 -b:a 96k -map "[split1scaled]" -c:v h264_nvenc -gpu 1 -2pass 0 -b:v 2500k -maxrate 5000k -bufsize 5000k -bluray-compat 1 -coder 1 -cq 0 -g 48 -level 4 -preset:v p7 -profile:v high -rc:v vbr -rc-lookahead 20 -tune:v hq "output_1080v4.9.mp4" -map "[asplit2]" -c:a aac -profile:a aac_main -b:a 96k -map "[split2scaled]" -c:v h264_nvenc -gpu 2 -2pass 0 -b_ref_mode:v middle -preset:v p7 -profile:v 2 -qp 30 -rc 0 -rc-lookahead 20 -tune:v hq "output_720v2.1.mp4"
Corresponding VoPro Scene would be something like this: 3-GPU.scene.zip This cannot yet be tested due to the current bug (as of version 0.7.4).