Multiple Page Libraries on site

Hi everyone

I have a strange issue that I haven't come across before.  A customer has got an old subsite on SharePoint Online that was created with the STS#0 template (classic Team Site with no group) and they want to modernise their old wiki pages.  This should have been straightforward as I was planning on using the https://learn.microsoft.com/en-us/sharepoint/dev/transform/modernize-userinterface-site-pages-powershell.

However, on this site they have two page libraries - the standard Site Pages library and then what looks like a custom page library (I've blanked out the name of the custom library as it contains the company name):

All of the pages they want to modernize are in the custom library but the issue with this is that the only content type available is Wiki Page:

This means that although the PnP PowerShell runs successfully against pages in this library, the new versions don't actually appear in the library.  I assume this is because the modern Site Page content type isn't available in the library.

I was under the impression that a site could only have one page library so I'm not sure how this site has the two.  On a more urgent note I need to work out the best way of modernizing these pages.  Currently the only way I can see is using Power Automate to copy the pages to the Site Pages library and then convert them there.  The only issue with that is that there are links within the pages to other pages so I'd need to go through them and fix these once they've been moved.  here are over 300 pages so I don't really want to do this.

Does anyone have any ideas on the best way forward with this.  Also, if you know how there are multiple page libraries I'd be keen to hear it as I haven't come across this before.

Thanks in advance for your help.