Thank you. I executed duplicati-cli system-info and realized that in my system there is a .config/Duplicati/updates/ folder in my home directory (with no updates), beyond the /usr/share/Duplicati/updates/ folder (with the new beta update).
So indeed it seems that the GUI takes the update from /usr/share/Duplicati/updates/, while the cli takes ~/.config/Duplicati/updates/.
I tried to copy the beta update from /usr/share/Duplicati/updates/ to ~/.config/Duplicati/updates/ and relaunched the cli command. Now I get the error:
Mono.Data.Sqlite.SqliteException (0x80004005): Attempt to write a read-only database
attempt to write a readonly database
at Mono.Data.Sqlite.SQLite3.Reset (Mono.Data.Sqlite.SqliteStatement stmt) [0x00084] in <5874f0c55a674ffc901a91a755e391d7>:0
at Mono.Data.Sqlite.SQLite3.Step (Mono.Data.Sqlite.SqliteStatement stmt) [0x0003d] in <5874f0c55a674ffc901a91a755e391d7>:0
at Mono.Data.Sqlite.SqliteDataReader.NextResult () [0x00104] in <5874f0c55a674ffc901a91a755e391d7>:0
at Mono.Data.Sqlite.SqliteDataReader..ctor (Mono.Data.Sqlite.SqliteCommand cmd, System.Data.CommandBehavior behave) [0x0004e] in <5874f0c55a674ffc901a91a755e391d7>:0
at (wrapper remoting-invoke-with-check) Mono.Data.Sqlite.SqliteDataReader..ctor(Mono.Data.Sqlite.SqliteCommand,System.Data.CommandBehavior)
at Mono.Data.Sqlite.SqliteCommand.ExecuteReader (System.Data.CommandBehavior behavior) [0x00006] in <5874f0c55a674ffc901a91a755e391d7>:0
at Mono.Data.Sqlite.SqliteCommand.ExecuteDbDataReader (System.Data.CommandBehavior behavior) [0x00000] in <5874f0c55a674ffc901a91a755e391d7>:0
at System.Data.Common.DbCommand.System.Data.IDbCommand.ExecuteReader () [0x00000] in <22e3c01ef2924ed2a1e251e05ed2871e>:0
at Duplicati.Library.Main.Database.ExtensionMethods.ExecuteScalarInt64 (System.Data.IDbCommand self, System.Boolean writeLog, System.String cmd, System.Int64 defaultvalue, System.Object[] values) [0x00061] in <c6c6871f516b48f59d88f9d731c3ea4d>:0
at Duplicati.Library.Main.Database.ExtensionMethods.ExecuteScalarInt64 (System.Data.IDbCommand self, System.String cmd, System.Int64 defaultvalue, System.Object[] values) [0x00000] in <c6c6871f516b48f59d88f9d731c3ea4d>:0
at Duplicati.Library.Main.Database.LocalDatabase..ctor (System.Data.IDbConnection connection, System.String operation) [0x0005e] in <c6c6871f516b48f59d88f9d731c3ea4d>:0
at Duplicati.Library.Main.Database.LocalDatabase..ctor (System.String path, System.String operation, System.Boolean shouldclose) [0x00007] in <c6c6871f516b48f59d88f9d731c3ea4d>:0
at Duplicati.Library.Main.Database.LocalListChangesDatabase..ctor (System.String path) [0x00000] in <c6c6871f516b48f59d88f9d731c3ea4d>:0
at Duplicati.Library.Main.Operation.ListChangesHandler.Run (System.String baseVersion, System.String compareVersion, System.Collections.Generic.IEnumerable`1[T] filterstrings, Duplicati.Library.Utility.IFilter compositefilter, System.Action`2[T1,T2] callback) [0x00078] in <c6c6871f516b48f59d88f9d731c3ea4d>:0
at Duplicati.Library.Main.Controller+<>c__DisplayClass28_0.<ListChanges>b__0 (Duplicati.Library.Main.ListChangesResults result) [0x0001c] in <c6c6871f516b48f59d88f9d731c3ea4d>:0
at Duplicati.Library.Main.Controller.RunAction[T] (T result, System.String[]& paths, Duplicati.Library.Utility.IFilter& filter, System.Action`1[T] method) [0x00271] in <c6c6871f516b48f59d88f9d731c3ea4d>:0
at Duplicati.Library.Main.Controller.ListChanges (System.String baseVersion, System.String targetVersion, System.Collections.Generic.IEnumerable`1[T] filterstrings, Duplicati.Library.Utility.IFilter filter, System.Action`2[T1,T2] callback) [0x0003e] in <c6c6871f516b48f59d88f9d731c3ea4d>:0
at Duplicati.CommandLine.Commands.ListChanges (System.IO.TextWriter outwriter, System.Action`1[T] setup, System.Collections.Generic.List`1[T] args, System.Collections.Generic.Dictionary`2[TKey,TValue] options, Duplicati.Library.Utility.IFilter filter) [0x0013a] in <04206d56f2084515b87543fcb90a7e00>:0
at (wrapper delegate-invoke) System.Func`6[System.IO.TextWriter,System.Action`1[Duplicati.Library.Main.Controller],System.Collections.Generic.List`1[System.String],System.Collections.Generic.Dictionary`2[System.String,System.String],Duplicati.Library.Utility.IFilter,System.Int32].invoke_TResult_T1_T2_T3_T4_T5(System.IO.TextWriter,System.Action`1<Duplicati.Library.Main.Controller>,System.Collections.Generic.List`1<string>,System.Collections.Generic.Dictionary`2<string, string>,Duplicati.Library.Utility.IFilter)
at Duplicati.CommandLine.Program.ParseCommandLine (System.IO.TextWriter outwriter, System.Action`1[T] setup, System.Boolean& verboseErrors, System.String[] args) [0x00313] in <04206d56f2084515b87543fcb90a7e00>:0
at Duplicati.CommandLine.Program.RunCommandLine (System.IO.TextWriter outwriter, System.IO.TextWriter errwriter, System.Action`1[T] setup, System.String[] args) [0x00002] in <04206d56f2084515b87543fcb90a7e00>:0