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No, you cannot save a 'decode as' instruction in a pcapng.

But you can add a comment to a pcapng.
And provide the 'decoce as' as a command line option -d. For example:

wireshark -d tcp.port==8888,http -r myfile.pcapng &

So it is possible to create a little script that launces Wireshark with the (temporary) decode as setting. (E.g. based on some info in the filename or extract the comment with tshark.)