I accidentally deleted all the contents on my Project.toml file. Will that affect my package updating?
You mean ~/.julia/environments/v1.x/Project.toml? Yes. You will just need to pkg> add or pkg> dev whatever you had there.
Theoretically this particular Project.toml it could be regenerated from the corresponding Manifest.toml but I am not aware of existing functionality for this.
In 1.4 you will be able to instantiate a lonely Manifest.toml (assuming there are no packages with the same name) and all packages in it will be put into a new Project file.
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Do you mean i need to reinstall all packsges?
They should be in your depot unless you did pkg> gc or similar, you just have to add them. So no downloading/rebuilding should be necessary.