Will a journal reject a paper for citing an Encyclopedia?
No
If other secondary sources like review articles are acceptable, then an encyclopedia is acceptable.
If the information is a well-documented, undisputed territorial boundary, then secondary sources should be adequate.
Personally, I have never heard of a paper being rejected for citing the wrong type of source in my field of research.  If the source is wrong or irrelevant, that could be a problem, but type of source does not matter.  In physics, non-peer reviewed sources like ArXiv can be cited, and these are less reliable than encyclopedias.