Local bookmarks are only allow defining a local and remote path, for this to work with synchronized browsing the bookmark would need to be capable of supporting two local folders and currently this is not possible. This is something we can consider for future releases but there are currently no immediate plans to change this.
Further investigation on this issue has revealed that synchronized browsing does not work as expected in the FlashFXP v4.x code base, both local panes switch to the identical path in both browsers when changing directories. This appears to be a design limitation in v4.x, This limitation does not appear in FlashFXP v5.x. There are no plans to backport these specific changes to v4.x.
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