You could remove GLT sub-bricks from an output bucket dataset using the 3dbucket command. This would be something like the following triplet of commands:
3dbucket -prefix FRED INPUT'[0..21,24..$]'
3drename INPUT INPUT_old
3drename FRED INPUT
assuming you want to excise sub-bricks #22-23 (recall that counting starts at 0 in AFNI). Then you should be able to re-run 3dDeconvolve with the -xrestore and -bucket options to continue appending new GLT results to the now-modified INPUT+orig dataset.