I'm not sure about that to be honest. I believe all tablepress information is stored within the shortcode. But I think it's probably not the tablepress shortcode causing the issue there, I recall testing it just a few days ago, and it worked okay.
There is a Remove these shortcodes options box right below the execute shortcodes option: https://i.imgur.com/7NPtr7D.png
If you use any other shortcodes, try adding them there (just the shortcode name, not the carets, comma separated). These can include WooCommerce related shortcodes, page builder shortcodes or whatever you can find.
After that, save the options and try again, hopefully it will do the trick.
If it does not, then feel free to add temporary FTP and back-end details, and I will try to do a debugging through the indexing code to see where it might fail.Best,
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