The Application Package is a file (named XsolInOrder.xapx) which contains all available icons and application default values that can be used in XSOL InOrder models pointing at that file. The Model Package is part of the .eslx model file and contains icons available for use in the specific open model and user note images added to that model file. Icons need to be copied from the Application Package into the Model Package to be used in a model.
The Application Package's location is specified in the Packages field on the Popular tab of the Application Options window. To find this go to the Welcome tab and double click on the Options button.
In the Welcome tab double click on the Options button and go to the Available Icons tab. Search for the icon required by browsing, using the category or description, filters and press the Copy to model button. You can copy multiple icons to the model at once by holding down the Ctrl key to multi-select icons and then pressing the Copy to model button.
When the upgrade of the model file was done XSOL InOrder interrogated your old Mapping Images folder to collect any user note images that were part of the model. If they are not visible in the upgraded model then they were not found in the old Images folder (i.e. they did not exist). It is likely that during the upgrade you were presented with the option of aborting the upgrade when the images were not found but you chose to ignore the warning. This problem can be fixed by either deleting the upgraded .eslx file, placing the missing images in the old Images folder and reupgrading the original Mapping .esl file or by readding the missing images in the notes manually.
Within XSOL InOrder go to the Home Ribbon's Help section and select the drop-down arrow. Select the Welcome Page option.