What does "Kindly appreciate" means here -
Kindly appreciate that we don't do this work.
Is this a common phrase.
It doesn't actually mean anything, since "Kindly appreciate that we don't do this work" is the same as "We don't do this work". It is an old-fashioned and obsolete commercial usage.
A lot of these old usages survive in India although they have disappeared elsewhere. I suspect it is because many Indian people need to use English but fear that they lack fluency. Rather than risk being wrong they hew to the old forms.