apa: Yes it will get overwritten but I am working on doing file edits automatically so you don't have to worry about that. Even with any plugin that edits files, you will have to reinstall the plugin due to it opening and writing to a file.
Hyde: Nothing is broken, pay attention, my mod does a find and replace in templates, with custom themes, if that 1 line that my plugin is searching for has been altered in any way then it won't find it to add the new stuff. I will put instructions for editing your custom templates.
Open forumbit_depth2_forum template
Find:
<img src="{$theme['imgdir']}/{$lightbulb['folder']}.gif" alt="{$lightbulb['altonoff']}" title="{$lightbulb['altonoff']}" class="ajax_mark_read" id="mark_read_{$forum['fid']}" />
Replace with:
<if $mybb->settings['enable_pl9ForumIcons'] then>
<if $forum['forum_icon'] then>
<img src="{$forum['forum_icon']}" alt="{$lightbulb['altonoff']}" title="{$lightbulb['altonoff']}" class="ajax_mark_read" id="mark_read_{$forum['fid']}" />
<else />
<img src="{$theme['imgdir']}/{$lightbulb['folder']}.gif" alt="{$lightbulb['altonoff']}" title="{$lightbulb['altonoff']}" class="ajax_mark_read" id="mark_read_{$forum['fid']}" />
</if>
<else />
<img src="{$theme['imgdir']}/{$lightbulb['folder']}.gif" alt="{$lightbulb['altonoff']}" title="{$lightbulb['altonoff']}" class="ajax_mark_read" id="mark_read_{$forum['fid']}" />
</if>
If you do those edits to your other 3 themes then it will work find on all themes.