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I would avoid cutting it until u have no other choice. It is pretty well impossible to repair afdterwards and the support the liner gives may be permanently compromised.
Try to determine if it is the hard plastic tongue or the edge of the tongue cutting in or say a seam or sewing that is troubling u. If u go to a shop u will have to determine this anyhow.
One trick is to use no sock, get in the boot over tighten it, ghive it some time and then take off the boot and find the red spot on your foot that usually come up from contact . So is the problem a contact point, a blood vessel or nerve being pinched or just pressure from a hi instep?
Is it the boot shell or the liner issue...?
Another trick is lipstick... put a contrasting lipstick colour on your foot where it is going to hurt or where the " red spot showed up. Don't smear iot up . TIght up the boot and go tru it again.. Now look where the libstick stransferred onto the liner - or the shell. Those will be the spots that need grinding or whatever. Can u reposition the buckle or lengthen it ? Run some tests. Does it hurt wearing the liner with out the shell ?
To soften a tongue a shop/ good boot fitter can grind the tongue fo that it flexes or becomes softer. So it is most important to to debug the problem before chopping up the boot.
If u don't have custom footbeds (about $150) from a good bootfitter - u may want to look into that first. Good luck