I’m planning to migrate my notes and knowledge base from Logseq to Obsidian and want to avoid common issues during the process. Are there any potential problems with links, block references, tags, embeds, queries, or plugins that I should be aware of? I’d also appreciate any tips for preserving note structure and metadata to ensure a smooth transition.
I’d suggest just trying it.
Make a test vault and see how it goes. If something goes wrong, it will be easier for someone to suggest a specific fix. If something goes wrong, you still have the original notes, and you can try again.
And if everything goes smoothly, no one has to write out a guide for all the things that might go wrong. 
Make a backup first if possible and necessary, and just have a go.