I would argue that the two verses are not talking about the same thing. The verse in 45:18 is saying that the brothers will eat of the fat of the land. It is not talking about the land itself; it is talking about what the land produces. The term for describing the best that the land produces is חלב הארץ.
The verse in 47:6, by contrast, is discussing the land itself. The discussion there is about where they will live (הושב, ישבו). They will live in the best part of the land, and the term to describe the best part of the land is מיטב הארץ.
Alternatively, we can explain that the two terms are referring to different people. When the verse specifies חלב הארץ it is referring to the brothers. When it specifies מיטב הארץ it is referring to Yaakov. As Chizkuni (to 47:6) explains, the verse in 47:6 should be broken up differently. It is saying that Yaakov should dwell in the מיטב הארץ because he is old and simply desires rest and good air. The brothers, however, will dwell in Goshen which is suitable for their pasturing needs.
במיטב הארץ הושב את אביך כי הוא זקן ואינו מבקש רק מנוחה ואויר טוב אבל אחיך בחורים ישבו בארץ גשן ארץ מקום מרעה ואל תשיבני מן האתנחתא לומר שהיא מפסקת שהרי דוגמתו מצינו זבולן עם חרף נפשו למות ונפתלי על מרומי שדה
Thus, חלב הארץ in 45:18 may have been referring specifically to the brothers, and not Yaakov.