Custom post type removing /page/2/ from URL when trying to access it

Are you making changes to the query in the template at all? If you modify the main query you often have to include “Paged” parameter, as explained here: https://codex.wordpress.org/Pagination

If WP_Query is altering the main loop and the “paged” parameter is not set you’ll need to add it with get_query_var(). This is so WordPress knows exactly what page it’s on.

It’s hard to know without seeing the code for the actual template you’re using, but that’s a potential path to explore.

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