Hello. in my experience, always click "Yes to all" to prevent error when go online. in this way, do you granted the infomation about hardware are the same, and dont lose " PLC configuration" for example.
Minimum version is 3.5 SP19 Patch 3. See https://store.codesys.com/en/codesys-git.html But you could ask your PLC vendor if it is possible to program their PLC's which have Runtime version SP16 with development version 3.5 SP19 or higher (should normally be possible, but with Safety PLC's there could be some regulation limitations).