This sounds like some very strange issues 
All planks and beams will sometimes randomly disappear from my hand for no reason when I'm building, usually after I've been using the <ENTER> /<RETURN> key for modular building and no matter what I do I can't get them to reappear in my hand. The only way to get them to reappear is to reconnect to the server.
What do you mean exactly with "disappearing from your hand"? Is the item really gone, i.e. it's no longer in your inventory or no longer equipped? Or is just the plank preview missing?
Someone experienced an issue related to modular building which caused a plank to attach to a different construction part, is this maybe the same thing that's happening here?
This is the most annoying one of them all because it causes the most frustration and headaches ESPECIALLY with blueprints! When removing planks and beams with a crowbar or deleting planks and beams with an axe or any other tool, you would think that the appropriate action would result in the appropriate result
Hmm... what do you mean this issue especially occurs with blueprints? Do you mean that this issue only occurs when trying to remove construction elements which were placed via blueprint?
How many construction elements does your blueprint consist of?
Java is a huge security risk that ideally nobody should have installed on their computer if they can help it
This isn't entirely true: You only have to worry about browser plugins (which are installed separately), this is the only situation where "security holes" actually matter. Web applications (in case of Java, Web Start or Applets) are executed with limited permissions, but due to security holes a malicious app could infect your machine. This also applies to other browser plugins, like Flash 
However, nowadays Java Web Start or Applets aren't used anymore, so in most browsers, these plugins are either disabled by default, or not supported at all.
Having Java installed on your machine is totally safe. If you execute a malicious program on your machine (no matter if this application is written in Java, C++ etc), the program does not have to abuse any "security holes" to infect your system, since it automatically gains full access to your computer.
Nevertheless, the Steam Version of Rising World is shipped with a JRE, so you don't have to install it on your machine. Having Java installed on your machine is only a requirement if you run the standalone (non-Steam) version 