If an emission factor (EF) is no longer included in the Annex I of the updated ISCC EU System Document 205 "Greenhouse Gas Emissions" (version 4.1), can I use the value from the previous System Document 205 (version 4.0)?

No, this is not permissible. In the updated ISCC EU System Document 205 "Greenhouse Gas Emissions", emission factors were removed either because they can be found in the Implementing Regulation (EU) 2022/996 or because they were deemed invalid, such as values from biograce. In cases where an emission factor is not listed in the Implementing Regulation, System Users are required to seek alternative sources. If alternative emission factors are used, they must be properly justified and highlighted in the documentation of the GHG calculation to facilitate the verification by auditors. For more information on requirements for alternative values, see here.