Why did all my inventory items merge as non-inventory when switching from Desktop to Online?

NO...this issue was NOT resolved.

After multiple phone calls with various individuals at Intuit I have now learned that if a company HAS inventory, it will be translated from an Inventory Item to Non-Inventory almost every time. QBO does not recognize Inventory Items, due to the merge process. If your Sales people were award of this fact and had informed me of this, I would have designed a MUCH different system moving from QB Enterprise to QB Online. Now 5 months of research and work completed to get our file ready to transfer has been washed down the drain. My file has been corrupted in the merge and cannot be used in its current form. The chart of accounts is not being recognized, several inventory parts were listed as Deleted in the program and my customer data has been corrupted. We are going to have to either re-merge our company file at the risk of getting the same results or go back to the beginning and design a new configuration. This means I will ALSO need to re-input ALL of the data from January after we come up with a system that will get our website talking to our accounting software and maybe an additional Inventory Application that will allow our company to HAVE inventory and conduct business. 

THANKS QuickBooks Sales Team!!! Perhaps upper management will start to see how important it is for your sales staff to actually KNOW the software and not just try to move units. 

Sorry, lorim28...there is no quick "work-around". The only option QBO provided was to manually open each items and switch it from "non-inventory" to "inventory" item. Since we had over 1,500 different parts, this was not an acceptable solution. That's when I found was SOS Inventory. This program was developed by people who had the same experience as us and found there was NO work-around, so they created their own software to work with QBO. This company is incredible. The software is very user-friendly and the support is like nothing I have ever found with any other company (no, I do not work for this company).  I highly recommend you take a look at the site. I found the staff to be very knowledgeable, honest and professional. You will not be sorry.