As a general rule, if you have modified any of the "original" Kunena source files (including the original
Blue Eagle template files) and replaced those files in your website, then you will lose those changes when you update from any version of
Kunena to another version of
Kunena. You will also lose any changes if you downgrade from one version of
Kunena to another version of
Kunena or even if you reinstall the same version of
Kunena that you currently are using.
If you want to preserve the changes you've made then you should create your own Kunena template; it depends on the extent of the changes you've made. When you say you've created a "heavily modified" customisation, it's not clear how you've achieved those modifications. If the changes only involve CSS then it
may be a better to create a separate file of CSS and load it from your Joomla site template with an
@import
directive (see also
How do I change the colours of my template in Kunena?
).
One
other way to preserve the changes is to backup the files from the
../components/com_kunena/templates/blue_eagle folder before you update from K 3.0.6 to K 3.0.7, but you will lose the other benefits of changes made in K 3.0.7 with the
Blue Eagle template. The other benefits may, or may not, be important to you; that's really a question that each person must answer for themselves.
I hope this information is of some help to you.