Before you apply these migration steps please make sure you back up your database and files web\web.config & DSC.config.
Here are the manual steps to migrate DotShoppingCart Suite V2.1 to V2.5.
1) Migrate database
2) Update web.config and DSC.config
a) Replace string "OpenSource" to "Commercial" in web.config and DSC.config
b) Remove table based shipping and table based tax configuration (see yellow background below) in DSC.config
<shippingServiceConfiguration defaultProvider="">
<providers>
<clear />
<addenabled="True" sortOrder="0" name="Table Based Shipping" type="DotShoppingCart.Commercial.Shipping.TableBasedShippingProvider" />
</providers>
</shippingServiceConfiguration>
<taxServiceConfiguration defaultProvider="">
<providers>
<clear />
<add name="Table Based Tax" type="DotShoppingCart.Commercial.Tax.TableBasedTaxProvider, DotShoppingCart.Commercial.Tax, Version=2.0.0.0, Culture=neutral, PublicKeyToken=null" />
</providers>
</taxServiceConfiguration>
c) Compare web.config and DSC.config in V2.5 to the existing ones and bring the new changes in V2.5 to the existing ones.
d) Go to Store admin and configure table based shipping and table based tax again