Tasks split using Resourse Usage change once published to PWA sever

Tasks split using Resourse Usage change once published to PWA sever.

Issue

Once I save, publish and close project the resource time allocation is jumbled on reopening the plan.

Questions

1. Does MS Project Professional 2013 and PWA allow saving and publishing of split tasks in project plans?
2. Is there any setting that needs to be changed?

Background

Our reoccuring projects have 7 stages (therefore 7 "tasks" in ms project) are are completed in a windfall process.

Project Planning is completed at stage level, with mutiple (1-4) resources assigned to each stage. The resources time for each stage is inputted and updated in the resource usage view.

I assign resources to task and then update resource time allocation in resource usage. Resources are either booked for 3.5hrs or 7hrs.