My initial idea of changing to use the rdkit internal JSON representation in the to_dict method doesn't seem to fix this as it also loses the hybridization info see extended example:

from rdkit import Chem
from gufe import SmallMoleculeComponent
settings = Chem.rdMolInterchange.JSONWriteParameters()
settings.useRDKitExtensions = True
# generate an rdkit molecule
ethane = Chem.MolFromSmiles("CC")
ethane = Chem.AddHs(methane)
Chem.rdDistGeom.EmbedMolecule(methane, useRandomCoords=False, randomSeed=0)
# check the state of each carbon
for atom in methane.GetAtoms():
    if atom.GetAtomicNum() == 6:
        print(atom.GetHybridization())

# create the SMC
smc = SmallMoleculeComponent(methane, name="methane")
# round trip to dict
smc_dict = smc.to_dict()
# remove the original object
del smc
smc_2 = SmallMoleculeComponent.from_dict(smc_dict)
# check the state again
for atom in smc_2.to_rdkit().GetAtoms():
    if atom.GetAtomicNum() == 6:
        print(atom.GetHybridization())

json_str = Chem.MolToJSON(smc_2.to_rdkit(), settings)
print(json_str)
json_mol = Chem.JSONToMols(json_str)[0]
for atom in json_mol.GetAtoms():
    if atom.GetAtomicNum() == 6:
        print(atom.GetHybridization())

SP3
SP3
UNSPECIFIED
UNSPECIFIED
{"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{},{},{"z":1},{"z":1},{"z":1},{"z":1},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[0,2]},{"atoms":[0,3]},{"atoms":[0,4]},{"atoms":[1,5]},{"atoms":[1,6]},{"atoms":[1,7]}],"conformers":[{"dim":3,"coords":[[-0.7455,0.0414,0.0117],[0.7473,0.0028,0.0012],[-1.1297,-0.6374,0.8144],[-1.1848,1.0255,0.1996],[-1.1998,-0.3346,-0.9388],[1.0841,-0.7365,-0.7731],[1.2266,0.9617,-0.268],[1.2018,-0.323,0.9531]]}],"properties":{"ofe-name":"methane"},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.4"}]}]}
UNSPECIFIED
UNSPECIFIED

So I think I just need to add this property to the to and from dict method.

Oh shoot, I'm glad we tried at least! Does rdkit have some kind of global settings similar to the pickle ones to tell it to include everything in its JSON representation?