Walter,
This takes me back to my days at Cummins with Track and Trace.
A few things from your answer.
1. The scanner - it has 4 things to your advantage, a. It's Android based, b. It has WiFi, c. It also has cellular, d. It has the ability to run custom apps.
Now the question is one of process flow. You can stick with the "docking station upload method" you describe - and it will work - but there are a few steps involved here in your process.
2. I do not know if there is WiFi in the Warehouse. If this is the case then I would write an app on the Scanner, that would transfer either:
a. Directly to your Database (if it is MySQL). This would eliminate the intermediate steps of first docking the unit, processing the
data from it, turning it into whatever format you require, sending it to the database server, decoding it there and inserting/updating your online database. You do however have a security risk here with MITM attacks.
b. Send it to a jRDC2 Server (that resides on the same Server as where your database is) and use jRDC2 Client in your scanner to send the data direct to the database. With this method you can do read/process/respond in real time, AND it is much safer security wise.
If you do not have WiFi in the warehouse, then I suppose the exercise would be one of determining cost of WiFi Range extenders as opposed to providing cellular data as opposed to how quickly (such as in FMCG) you need to have the data available for a next step.
There are so many ways of doing this that at the end of the day it will come down to what you are most comfortable with and what resources you have available to you when you commence with this project.
If you have private questions, PM me - I'll try and impart my experience with you like that if it is not for general public consumption.