I would use screc_cat (part of the SRecord tools) to join both HEX files into one in a post-build step. Despite it's name, the tool can process many formats - including HEX. J-Link driver installations in Windows come with a flashing tool, found under…
Replied to the thread Is there a way to change definitions of __INT32_TYPE__ and __UINT32_TYPE__?.Post> ... which is a system file and should not be edited. This is only relevant if you work with multiple toolchains and/or platforms in a project, and need to maintain source level compatibility. For my private projects, I do whatever I like.