I’ve always used Obsidian with folders that are accessed by other editing apps - it sits on top of such folders. I have never experienced a problem. And I often have a file open in five apps simultaneously.
There are a number of threads where people explain how they combine Logseq and Obsidian using the same folders.
I have checked out Logseq a few times and always uninstalled it fast. I find it too unstable for me.
The key issue with all programs that autosave or sync files is the risk of conflict of versions or saves. The message received by the OP indicates such a conflict, but there was no description of how autosave or sync was set up in either program. iirc Logseq’s default is to sync with Git. Obsidian’s default has autosave but no sync.