$A\cup B=C$
Suppose some function $f$ totally orders equivalence classes of $A$ and equivalence classes of $B$, both of which are formed by the same equivalence relation $\sim$.
The domain and range of $f$ is $C$
The range of $f$ in $A$ is $A$
The range of $f$ in $B$ is $B$
Does this imply that $f$ totally orders equivalence classes of $C$ formed by the same equivalence relation?
For a counter-example let $C=\{1,2,3,4\} , A=\{1,2\} $ and $B=\{3,4\}.$ Let the set of equivalence classes be $E= \{\{1,3\} , \{2,4\}\}.$
By "the equivalence classes of $A$" I assume you mean $\{x\cap A: x\in E\}$ \ $\{\phi\}.$ So the equivalence classes of $A$ are $\{1\}$ and $\{2\}.$ And the equivalence classes of $B$ are $\{3\}$ and $\{4\}.$
Suppose $\{1\}<\{2\}<\{4\}<\{3\}.$ This doesn't "translate" to a linear order on $E.$