In my experience with three companies at/with whom I worked, a re-skin is a means to either:
1) Apply a more brand identity quickly
2) Make incremental improvements to buy time for a fundamental re-design
3) “Do something” to show “progress” to internal stakeholders

When evaluating a re-skin opportunity, I would advise the designer to do two things:
1) Assess as best you can how congruent the current site architecture is with target audience(s) and with the stated online objectives of the company
2) Assuming congruence is lacking, ask whether a fundamental change such as a ground-up re-design is planned, and if so, by when

The golden opportunity is when a company is re-skinning a highly congruent web site to reflect a company re-branding

The biggest red flag is when a company wants to re-skin an incongruent web site to “to something”, acknowledges major usability or other issues with the current site, but no plans exist to re-design the site by an identified target date

I would rank opportunities that meet neither of the above descriptions somewhere in between the golden and the red flag scenarios just described.

Top hidden issues to look when evaluating a red flag or near-red flag opportunity:
1) Resources do not exist for a re-design of a highly incongruent site. This is a hallmark of a company that under-values or even devalues the potential of the Web Channel to achieve their business objectives. What is the long-term value of such a client to your practice? Probably not much
2) The internal political consensus does not exist to enable a fundamental re-design of an incongruent web site. What are the chances that the same lack of consensus will add to time, cost, and drama when executing a re-skin? Probably high

Caveat Vendor.