The Employee Rate Table is pre-setup in the software if you have the Manufacturing Modules licensed so there should have been no need for you to do this unless someone deleted it. No one should be deleting Shop Floor Control Tables (ie, Sys 31) if you have Manufacturing Installed. That makes me a little uneasy about the health of your system.
There is almost no relationship between Employee Time Entry in your HR system and the Manufacturing System. I strongly suggest your seek the help of a Professional for a couple of days as it looks as if you are on the tip of a proverbial iceberg! Your system needs a shakedown as it obviously is not Manufacturing-orientated.
The P00191 Generic Message/Rate Types must be setup in Manufacturing regardless of your settings in Manufacturing Constants. This is because the P311221 "Hours and Quantities" is hardcoded to only work with Employee Address Book Records entered in this Table. However, it only uses them when Manufacturing Constants are set. In cases where you use the Work Center Rate then the "Rate" in P00191 can be set to zero/blank but that Employee must still be in the Table if you are going to type their AB nbr into P311221.
In P00191 the Code is EIGHT characters long. If your Address Book codes are shorter as is likely then you must pad out the space with zero's, ie, "00008447" NOT "8447".
My expectation is that Cost Rollup R30812 will use the Employee setup on the Routing F3003 to retrieve the Rate. If your Manufacturing Constants say use the Work Center then it uses W/C Rates instead. However, these must be setup in the F3003 for this all to work. This may not be relevant to you. P311221 is also used by the CSMS Modules but the Accounting is handled differently.
...and NO. You don't need to reboot the Enterprise Server when Manufacturing Constants change. (When do you ever need to do that?) With all such Application Constants the worst case scenario only has you logging out and then in again.
Good luck.