These are all quite different operations.
1. 3drefit is not changing the data at all, just removing information from the header. This shouldn't have any effect on the slice timing.
2. 3dresample -orient LPI. This also loses the oblique information, but more importantly changes the definition of what a slice is (the 3rd dimension 'k') and if you include voxel resolutions or grids potentially introduces interpolation. This will make slice timing correction wrong unless your data is LPI in the first place.
3. 3dWarp - either of the obliquity options will change the oblique angle of the dataset and alter the data. Again slice timing correction will not be possible and wrong if used.
For more info on oblique datasets, see this link:
[
afni.nimh.nih.gov]
