Oh, that explains everything. Maybe an off-site crawl-type search could be the best solution for this case, as the content is not directly stored as wordpress content.
Don't forget that the lite and the pro version are two different plugins, so the lite version shortcode is not automatically replaced with the pro version shortcodes – both have different ones. So wherever you had the lite version shortcodes, you will have to replace them with the pro ones first. The Pro version can do exactly the same as the lite version, with much more options additionally.
The reason for separating the plugins was mostly much better compatibility and safer updates, plus anyone can go back to the lite version if needed.
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