One way this could work would be for the trainer option be saved into the config for a specific game, and then winuae checks the MD5 checksum of the ADF/IPF?whatever images and if they don't match then winuae ignores the trainer options (greys them out maybe).
If the MD5 does match then the trainer options are enabled. Naturally the user could "override" this if searching for new trainer options etc..
One hard aspect is knowing what trainer options winuae would support.. There are so so many possibilities.
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