A quick post explaining my approach based on several other posts in the AX community.
With regards to the "missing labels", it's all about making sure the AOS instance is stopped and started BEFORE you fire up the AX Client to perform the post actions after updating the Model Store. By doing this, you make sure that the label files are synchronized in the file system on the AOS server based on the newly updated labels in the Model Store.
So if You are faced with a form (The Model Store has been modified) showing only label ID's when launching the AX Client, close the AX Client and restart the AOS instance to force the synchronization. This was all I did to solve this.
Looking at the Event Log > Application, you should find an entry (Source > Dynamics Server nn, Event ID > 3002, Type > Information) with a description like this:
Object Server nn : One or more local label files are out of sync with the label files in the model store.
The AOS has copied the correct files to its local directory and the startup of the AOS will proceed.
Copies of files are made in: D:\Program Files\Microsoft Dynamics AX\60\Server\AXTech\bin\Application\appl\Standard\.
File(s) copied from the model store are: AxFPKar.ald;AxFPKcs.ald;AxFPKda.ald;AxFPKde.ald;AxFPKde-at.ald;AxFPKde-ch.ald;AxFPKen-au.ald;AxFPKen-ca.ald;AxFPKen-gb.ald;AxFPKen-ie.ald;... (truncated for better readability)