I think this is kind of okay, but I would look at the conditions this would make it possible that there are multiple states inside the region.
However, I fine with a TODO in that regard.

I don't think atm there's any possibility to get multiple states that are not true/false_branch so this check is mostly for sanity

Then a TODO should be sufficient.

I didn't understand, would you like to remove this check or would you like to check if there can be more that true/false branches inside?
The latter is checked above:

if not (
            isinstance(first_conditional_block, dace.sdfg.state.ConditionalBlock)
            and len(first_conditional_block.sub_regions()) == 2
            and isinstance(second_conditional_block, dace.sdfg.state.ConditionalBlock)
            and len(second_conditional_block.sub_regions()) == 2
        ):

I am not 100% sure, but very positive that you can remove this restriction, because of the check about the compatibility of the symbol mapping.

I would need to add a test though then and I'm not sure it's worth the time 🙈

I am fine without a test, because a Tasklet is, on the DF level a self contained object, as such it it not different from a Tasklet.

However, this does not handle symbol renaming in the subsets.
See also comment above.

The subsets can only have symbols or something else as well?

There is something missing here.
While in can_be_applied() you check if there are no symbol conflicts you never copy the symbols that are exclusive to the second conditional block.
Put it differently you detect the case where SDFG 1 has n := a + 1 and SDFG 2 has n := a - 1, but you do not handle the case where SDFG 1 has m := a + 1 and SDFG 2 has o := a + 1.
So you must copy them as well, for this you have to do something like:

missing_symbols = {sym2: val2 for sym2, val2 in second_cb.symbol_mapping.items() if sym2 not in first_cb.symbol_mapping}
for missing_symb, symb_def in missing_symbols.items():
    first_cb.symbol_mapping[missing_symb] = symb_def
    first_cb.add_symbol(missing_symb, second_cb.sdfg.symbols[missing_symb], find_new_name=False)

I have to figure out how to add this to a test 👍

I am pretty sure this information is already contained in second_arrays_rename_map.

I need to keep the reference to the node object though so I can find the corresponding new node in

                new_edge = first_inner_state.add_edge(
                    nodes_renamed_map[edge_to_copy.src],
                    edge_to_copy.src_conn,
                    nodes_renamed_map[edge_to_copy.dst],
                    edge_to_copy.dst_conn,
                    edge_to_copy.data,
                )

@iomaganaris This here is the location where you need the renaming of the data containers for naming the connectors into account.