I know there's a feature in AA that can you can multiple edit the values of Keystrokes, Object Cloning, Object Properties and Delays.
Is there any solution on how to fix within this problem? 
I can't afford time to search and look for all of lines one by one to change the values of it, especially your code line reaches around 5K+ it's really time consuming.
I had the same experience in the past and unfortunately there is no solution for that. I even tried manually editing the .atmx file but the XML inside is encrypted.
You might consider automating it, but that's probably not the answer you are looking for.
If you work with a lot of subtasks and variables, I sometimes go for passing only a single variable between tasks - an XML string containing all the variables you need. This has the benefit of maximum versatility, as you can keep adding and removing variables from the XML without changing the Run Task command settings. You can even pass lists, something AA doesn't support. The drawback for this is that in each task you need to have a few overhead lines of code for variable retrieval.
XML variable example:
<vars>
<var name="customer_id">C0123</var>
<var name="customer_name">John Doe</var>
<var name="customer_lang">EN</var>
<list name="customer_address">
<item>Street 132</item>
<item>City ABC</item>
<item>Country XYZ</item>
</list>
</var>
And the retrieval of a variable would look like this:
