Never, ever use Word to edit anything related to coding, it adds all sorts of hidden stuff that will break everything. You should stop the server, install DevTools, run /extractplugin PluginName for each plugin, copy the source code for each plugin from plugins/DevTools folder into plugins folder, delete the phar files as you will now run them from source code, get a GOOD text editor or a free IDE and edit all the plugin.yml files by adding [3.0.0-ALPHA5] to the api entry, then run the server. When you are finished you can run /makeplugin PluginName to make phar files. Most of your plugins we'll probably now break, your worlds might get corrupted, plugin data disappear, etc etc. So back up everything before doing everything above... Now you have to actually make sure that your plugins load and work correctly since bumping the API version only means pocketmine can try to load it. If you have come from a spoon the chances are you'll have to either fix the code yourself, or find updated versions. Poggit has has 4 or 5 of yours which should save you some time, and more coming soon.
Agreed with Awzaw, i personally use NetBeans IDE and also i usually use Sublime Text 3 to edit YAML and files with other extensions and also use Notepad ++.
MSpawns is definitely on Poggit, since i submitted it. EDIT: I just submitted an update to bump the API as i forgot, lol
Using an editor that adds invisible things to your code is not clever, and can waste everyone's time here on the forums. If the plugin.yml is invalid pocketmine should tell you, but either way if the OP uses Word to edit files (s)he is asking for trouble. If you edit your API versions correctly console output should show that PocketMine is at least trying to load them, although that's no guarantee they will actually load and work: for that you'll need to update the code too. And at the risk of repeating myself, not in Word. If they still fail to load, check the yml on http://codebeautify.org/yaml-validator Another possibility, given the lack of information you have provided, is that you left the original phar files in the PocketMine plugins folder, next to your new source code versions for which you edited the plugin.yml files. If you have both phar and source plugins, only the phar will load.