i haven't ever found any problems with migrations other than...

1) security on folders, which is easily reapplied
2) paths stored in the zen-cart database - of which i've only ever seen two, both of which relate to the location of the cache directory. once again, these are easily changed via phpmyadmin
3) add-on modules specifying path information explicitly rather than using already supplied definitions in configure.php

the 2 x configure.php files are very quickly edited, and i recently went through a migration from a non-ssl host to one with ssl. only problem i had was the domain ssl was purchased for (in this case it was purchased for domain.com rather than www.domain.com, hence i had to edit my configure.php files accordingly and now all ssl pages appear as http://domain.com/ in the browser).

hope this helps