This is my (bad) experience with the "Some mods are redundant" problem, which I have often:
Mod A contains file1, file2, file3. It was installed correctly.
Mod B contains a different file2, I want it overwrites file2 from Mod A, so I simply install Mod B and then I get:
"There are unresolved file conflicts"
"Some mods are redundant"
To solve the conflicts I select load Mod B "after (suggested)" Mod A, then click on "Save" and the conflict message is gone, but the "Some mods are redundant" message is still there so I check it and it says:
---
Mod name: Mod B
Deployed files (0)
None
Files overwritten by other mod (1)
file2 (Hash not calculated) - Mod A
Files not deployed (0)
None
Files that are supposed to be deployed but weren't found (0)
None
Files that are present but couldn't be read (0)
None
---
Conclusion: Mod B was not installed. To this day, I couldn't find a solution for this problem.