Dual boot is problematic. Ideally, you would want to have a portable-style Syncthing installation with auto-upgrade disabled that uses relative paths (with / forward slashes as they work both in Linux and Windows). This way, you will be able to run it inside both Linux and Windows and re-use the same database without worrying about incompatible versions, etc. You should be able to find more information on this type of setup if you search the forum for “dual boot”.
Also, when using NTFS in Linux, make sure to always enable “ignore permissions” in the Syncthing folder settings.