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I installed 1.6.3 some time ago. I modified some of the templates and added at least one plugin that required a template mod. Plus a bunch of CSS changes. I also modified the English language file, changed graphics. Added a button to insert BB code. Oh, and I also changed the folder where the admin page is stored.

I want to upgrade to 1.6.12 So that's jumping multiple versions.

How would you approach this project, assuming you were willing to throw out all the mods. I'm tired of trying to support all my mods, because it's too much trouble keeping track of them.
Well in case like yours, first of all i will make complete backup of my database and files, theme
Then i will find all files modified using File Verification and keep them in safe place
Then i can find all the changes in mybb fles using changelog so that i can make changes in latest version
http://docs.mybb.com/Versions.html
Restore the theme to default MyBB theme
After this i will upgrade my forum, install my old theme again and make changes to the files which are customized
This will be my approach
Edit: delayed response

put forum offline, take backup of database, themes (including templates), and files.
run file verification tool and take a note of changed files.
examine templates of the active theme and note changed templates.
install a local forum (in computer) and upgrade the live forum
re-modify the live forum as required based on noted changes and the local forum
Thanks for the tips. I'm not interested in retaining the mods I made. My only concern is to upgrade the forum without wrecking things. I'm afraid the changes I made might somehow interfere with the upgrade.
Create a text file and every time you make a core edit just put a note there so after upgrade you will know exactly which file you will have to edit again
Thanks. I have a folder with before and after versions of all my core edits. I can easily see the changes by using a file compare program. And I can easily modify new ones using the same type of software to see a side by side views.

My concern not preserving core edits. I do not care about preserving these. My only concern is upgrading the software without some change I made interfering with the upgrade. That's it.
Create a new DB and new folder with the new software and then run Merge System? Depends on what plugins and other edits, but that will preserve the existing stuff for sure
I used to be in your shoes....I got tired of the constant updates to versions, mods, etc...I go with a pretty vanilla board now just to make the headaches go away.
I think people here were trying to help me preserving my template mods. As I mentioned above, I was not interested in preserving them. I was sick of having to think about them every time I upgraded.

Anyway, here's how I handled it. I installed a new default forum elsewhere. I copied its global CSS to a text file. I also copied my modified CSS to the text file. Then compared them using file-comparison software. This let me see the CSS elements side by side. So I copied my elements over to the default CSS one at a time, but only where I thought it would not disrupt the way a default template uses it. Then loaded it in the test forum and made tweaks here and there.

After that I loaded this new theme into my modified forum. Did some touch up. Then upgraded the forum to the latest version. And because my theme was in shape to accept this, it went smoothly. Well, mostly. I had to make minor touch up.

It's amazing how much CSS can control the look of a forum. Even though I'm using 100% default templates now, it still looks a lot like it did before. I attached before and after shots.
During an upgrade, your template/CSS changes to themes aren't going to go anywhere. If you're really worried, after taking a database backup, simply export your theme to a XML (in the ACP), and if your changes are reverted after the upgrade, you can simply import your theme.
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