That full menu only resets because (I assume) you are including the full menu.dif as exported. Instead, edit it (using a text or xml editor) to include only the options you want to change.

eg. this menu adds an Import Invoices to the Invoicing / Invoices menu:

<?xml version="1.0" encoding="utf-8"?>
<changes xmlns:xsi="">www.w3.org/.../XMLSchema-instance" xmlns:xsd="">www.w3.org/.../XMLSchema">
<option guid="320108c1-0e09-48c1-af25-2bca6d5ac231">
<changes xsi:type="CreateChange" name="Import Invoices" optiontype="VBForm" navigationItemType="Form" Position="6" parent="05051b81-d865-4c91-917f-29bb5456a80a">
<Parameters>
<parameter name="FeatureTargetGuid">1c73c9bd-8c2d-4277-af12-5b679ca8c8ec</parameter>
<parameter name="icon" />
</Parameters>
</changes>
<changes xsi:type="ShowChange" />
<changes xsi:type="SetIconChange" iconname="" />
</option>
</changes>

thank you Geoff, I will try it out

Hi Geoff, this is correct answer. However, each of the user is also amending my customization menu name text on their own PC/Sage 200 desktop app, so when they apply the sdbx updates again, the customized menu name will reset.

Is there anyway for customer to import their own diff file again after update?

I doubt that is possible, you can only import via and SDBX

I agree with Toby. They'd have to export the menu, package it as an add-on (sdbx) then import it that way.  And it would probably then lose any changes you've made!