Can Quartus Prime 16 detect changes in sources to show the build is out of date?

Besides the message you mention, what is your indication that changes you've made to the design are not being implemented? Have you tried programming a device with the updated design?

Moving a project from Standard to Lite is a tricky prospect if devices, IP, or features only supported in Standard were used in the design.

If it's really not working, even after cleaning the project (or manually deleting the db and incremental_db directories), you could try creating a new project and bringing the source code and assignments into it.

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