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The phrase "affected differently" is correct and usable in written English.
It can be used to describe how different subjects or entities experience varying impacts or changes due to a particular factor or event.
Example: "The new policy affected differently the employees in various departments, leading to diverse reactions and adaptations."
Alternatives: "impacted in distinct ways" or "influenced differently".
Exact(60)
Individual species' leaf litter decomposition can be affected differently by different cities.
When plants were transferred to cold the diurnal cyclic pattern was affected differently for different metabolites.
We wanted to understand whether CEC and CEP levels are affected differently by different chemotherapy agents.
Erwinia amylovora (MTCC 2760) affected differently using different solvents of the test plant.
Propagation of [PSI+] and [URE3] prions was affected differently by the different Hsp70s, which uncovered additional distinctions among the Hsp70s.
To conclude, we have demonstrated that peptide amyloid aggregation can be affected differently by two chemically different families of cosolutes.
Future developmental functions may be affected differently by exposure at different developmental stages.
These models showed that affective experiential versus acceptability perceptions have different explanatory composition and are affected differently by information.
(4) These policies would result in competitiveness issue and rebound effects, wherein different countries would be affected differently.
Visual and olfactory signals are very different in nature and are affected differently by environmental factors.
Cool-season crops differed in resource use, which therefore affected differently the following second crop.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com