In what ways could this affect me in the future?

Then repeat the process.

While the value is indirectly affected by the business that is run through it by making it more valuable to investors, @John Underwood is correct, most of the time it's going to be appraised based on residential sold comps.

Try and learn from this - what mistakes were made and what was overlooked, so you don't repeat them.

Live in the property for 2 years (to avoid paying capital gains, if for some reason you have to sell the home within 5 years of owning it) then use the money you have saved to buy your next property and go live in that new property, rinse and repeat. 

I Agree, pay the extension fee and note where you went wrong in your timeline of construction so you can help not repeat the mistake.

The logic behind this is that the appraiser will give more value to the home and you have just affectively financed a new roof.

Everything is synchronized through iGMS.com and really makes my life simple and easy and hopefully will help bring in more repeat revenue. 

It affects landlords.

There is the option to list the house for sale still occupied, but this will probably scare off some buyers and affect the quality of offers I get.