I have experienced difficulties getting the target device selection to “stick”, that is, be set and saved properly once set.
One normally sets the target device by navigating through this menu sequence:
Project -> Properties -> C/C++ Build (left list) -> Settings (left list) -> Target (tab)
There are several drop-down lists on this tab that let you select device Series, MCU, and Board.
I have found that this setting is often distorted, reverted or otherwise not set properly if I change it. This is especially true if I’m using Eclipse’s “Build Configurations” capability so I can have several different build configurations for a single project (e.g. different #defines and compiler settings for a “Debug” configuration vs. a “Release” configuration).
These problem(s) existed in the 1.10.x version of the AC6 tools, I just got the 1.11.x update today but have not checked to see if this issue has been fixed.