Logseq has the ability to find files in subfolders, so it’s not necessary to move all of your Markdown files to the pages folder.
For me logseq has created its own nested file structure , but does not seem to be able to read down into it.
https://discuss.logseq.com/t/many-journal-pages-disappear-nested-directory-structure/11289/2
Could it be because it finds the deeper pages folders, but not the journals?