Calling cacheManager->refresh() with no arguments will delete almost all of the cache files (but takes some time). It can be called with arguments to selectively delete parts of the cache.
I'm not sure about reloadContext(). I think it just refreshes the resource map for that context. I don't believe it affects the cache at all. It's a fairly fast way of getting MODX to recognize a newly created resource -- the OP's original problem.
No MODX function that I know of deletes *all* the cache files. There is an extra called
CacheClear that does. It's faster because it does no permission checks and simple unlinks everything in the cache directory. I think you could install it and just add this to your code:
$modx->runSnippet('CacheClear');
Remember that the next visitors to your site will see a slowdown because the cache is empty. One of the reasons cacheManager->refresh() takes so long is that it recreates some of the cache files.