So I tried my earlier suggestion and this is my findings.
Developer 1 makes the change to the db and does a db first sync in the LLBLGen designer getting the model in sync.
He/she then checks in the project file, which create a patch like this:
--- a/src/TheHub.Entities.llblgenproj
+++ b/src/TheHub.Entities.llblgenproj
@@ -223,6 +223,7 @@
           <Field Name="DaysBeforeEmail" Type="int" IsOptional="true" Precision="10" />
           <Field Name="Description" Type="string" IsOptional="true" MaxLength="100" />
           <Field Name="Key" Type="int" Precision="10" IsPrimaryKey="true" />
+         <Field Name="NewCol2" Type="int" IsOptional="true" Precision="10" />
           <Field Name="SetByUserId" Type="string" IsOptional="true" MaxLength="50" />
           <Field Name="SetLocalDateTime" Type="datetime" IsOptional="true">
             <OutputSettingValues>
@@ -6858,9 +6859,9 @@
         <Sequence Name="@@IDENTITY" />
       </SystemSequences>
       <Catalogs>
-       <Catalog Name="TBH" SyncSource="1">
+       <Catalog Name="TBH">
           <Schemas>
-           <Schema Name="dbo" SyncSource="2" LastSyncWithDatabase="2019-05-03T19:27:38.2502937Z">
+           <Schema Name="dbo" SyncSource="2" LastSyncWithDatabase="2019-05-10T12:36:13.2432922Z">
               <Tables>
                 <Table Name="HSE_ALERT">
                   <PkConstraintName Name="PK__HSE_ALER__4A5467AC32774862" />
@@ -6875,6 +6876,7 @@
                     <Field Name="set_local_dtm" Ordinal="8" IsOptional="true" DbType="4" />
                     <Field Name="alert_description" Ordinal="9" IsOptional="true" DbType="12" Length="100" />
                     <Field Name="days_before_email_nbr" Ordinal="10" IsOptional="true" DbType="8" Precision="10" />
+                   <Field Name="new_col2" Ordinal="11" IsOptional="true" DbType="8" Precision="10" />
                   </Fields>
                 </Table>
                 <Table Name="HSE_ARCHIVE_CLAIM">
@@ -13169,6 +13171,7 @@
             <FieldMapping FieldName="DaysBeforeEmail" TargetFieldName="days_before_email_nbr" />
             <FieldMapping FieldName="Description" TargetFieldName="alert_description" />
             <FieldMapping FieldName="Key" TargetFieldName="alert_key" SequenceToUse="SCOPE_IDENTITY()" />
+           <FieldMapping FieldName="NewCol2" TargetFieldName="new_col2" />
             <FieldMapping FieldName="SetByUserId" TargetFieldName="set_by_user_id" />
             <FieldMapping FieldName="SetLocalDateTime" TargetFieldName="set_local_dtm" />
           </FieldMappings>
Developer 2 does a pull and cherry picks the changes from the project file ignoring the Field in the Table and deleting the 
TargetFieldName="new_col2"
in the FieldMapping.
He/she then opens the project in the LLBLGen designer and does a model first sync which identifies the chang.
Then does a Generate Update schema and gets
ALTER TABLE [dbo].[HSE_ALERT] 
    ADD [NewCol2] [int] NULL
Which can then be applied and finally reverts the cherry pick and does a normal pull/merge.
This seems to work and I suppose some of this could be automated (i.e. the cherry pick and editing of the llblgen project file).