The use of Auto Number Format is almost entirely useless this part of the metadata is not included in the exported solution files, and that appears to be the case.
In a completely new instance (build 2136) I have created a solution with an entity, and an auto number attribute. The attribute works and is numbered according to the metadata I defined.
Exporting the solution gives this information for the attribute:
<attribute PhysicalName="new_number2">
<Type>nvarchar</Type>
<Name>new_number2</Name>
<LogicalName>new_number2</LogicalName>
<RequiredLevel>none</RequiredLevel>
<DisplayMask>ReadOnlyInUI|ValidForAdvancedFind|ValidForForm|ValidForGrid</DisplayMask>
<ImeMode>auto</ImeMode>
<ValidForUpdateApi>1</ValidForUpdateApi>
<ValidForReadApi>1</ValidForReadApi>
<ValidForCreateApi>1</ValidForCreateApi>
<IsCustomField>1</IsCustomField>
<IsAuditEnabled>1</IsAuditEnabled>
<IsSecured>0</IsSecured>
<IntroducedVersion>1.0</IntroducedVersion>
<IsCustomizable>1</IsCustomizable>
<IsRenameable>1</IsRenameable>
<CanModifySearchSettings>1</CanModifySearchSettings>
<CanModifyRequirementLevelSettings>1</CanModifyRequirementLevelSettings>
<CanModifyAdditionalSettings>1</CanModifyAdditionalSettings>
<SourceType>0</SourceType>
<IsGlobalFilterEnabled>0</IsGlobalFilterEnabled>
<IsSortableEnabled>0</IsSortableEnabled>
<CanModifyGlobalFilterSettings>1</CanModifyGlobalFilterSettings>
<CanModifyIsSortableSettings>1</CanModifyIsSortableSettings>
<IsDataSourceSecret>0</IsDataSourceSecret>
<Format>text</Format>
<MaxLength>100</MaxLength>
<Length>200</Length>
<displaynames>
<displayname description="Number 2" languagecode="1033" />
</displaynames>
<Descriptions>
<Description description="" languagecode="1033" />
</Descriptions>
</attribute>
The number format is nowhere to be seen.