Please refer to this topic to see how to copy items from a FLA: Scripting the import of a moviefile (for animation-reference) .
I think you're gonna have to make use of some third party application to help you suppress this warning, like or Mouse Recorder - Macro Recorder - Windows Automation or https://autohotkey.com/ . You can create a script that dismiss the warning and then call it with JSFL.
Furthermore, try to contact Adobe support or request this feature at: Adobe Animate CC Feature Request/Bug Report Form .
Sigh, okay, so as an FYI, copying items (fl.copyLibraryItem) will suffer the same warning. It seems to me that the mechanism for Animate to open an FLA for any reason uses the same code path, which essentially will encounter the warning regarding not using the latest Adobe AIR version.
I actually worked around this warning in a slightly convoluted way, but it works. I essentially:
-Traverse all the installed players and find the highest Air version
-Create an XFL via bash script (I execute this from JSFL)
-Load PublishSettings.xml
-Modify and save
-Load the XFL
I will eventually save it as an FLA.
I'll have to see if I can work through the other scenarios.
I'll contact Adobe Feature Request/Bug Report. Unfortunately I don't have tremendous faith that they will want to address this, but one never knows.
Thanks again for your suggestions.