Indeed, the library which contains the initialisation code was reloaded between the calls which caused the initialization-routine to be run twice, but not my checks if it's the same Display.
Sorry for the mess, it seems to work fine now.
Now just a bit of polishing and a lot of testing, and maybe there'll be a vaapi transcoding version of vlc soon.

Hi,
    From the tracelog it seems that both the decoding and encoding call
the function of vaInitialize, which will initialize the different
display context for decoding and encoding. In such case the surface ID
can't be shared correctly between decoding/encoding.
    Will you please also call the vaInitialize only once for
decoding/encoding and then see whether it is helpful?

Best regards.
     Yakui

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