I have obsolete entries in my svn:mergeinfo from are already deleted branches. Is there a way to clean the entries in svn:mergeinfo?
Automatic way? No, there isn't. But you can do it by hand, either using
svn propdel svn:mergeinfo path/to/dir
if you want to delete the complete mergeinfo, or
svn propedit svn:mergeinfo path/to/dir
if you want to change just some lines.
However, I highly recommend that you delete/modify the property only where it really does not make sense. For example, in a typical svn repository layout,
/
/trunk
/tags
/tags/t1
/tags/t2...
/branches
/branches/b1
/branches/b2...
the svn:mergeinfo property should only be set on the trunk node and the branch root nodes (i.e. /branches/b1 etc.). If you never merge between anything else but the trunk and the branch root nodes, you can usually safely delete all mergeinfo properties on other files.
A final note: if the only place where svn:mergeinfo is bothering you is trunk, that stop here and now. It is just too much of a hassle with too little gain :)