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Restoration
During the original colour restorations, the team were keen to present the episodes as close to the original broadcast master tapes as possible, as explained by senior Restoration Team content producer Steve Roberts:

"One thing which the team had to constantly be wary of was the temptation to not just restore, but to also improve on the original. For instance, during the scene in which the Silurian is about to attack Liz Shaw in the barn, there are annoying white ‘edit-flashes’ at each picture cut. This was due to the way the original film sequences had been spliced together, and it would have been very easy to take out a frame at the beginning of each new shot to remove them. However, this would not be in the spirit of restoration, and the viewer would not be seeing a fair representation of the story as it originally was.'"

In 1997, whilst working on the VHS release of The War Machines, the approach of straight restoration, that of returning the episodes to their original state, became compromised by the desire to improve upon what was originally broadcast. Sound engineer Mark Ayres explained the difficulties:

There are some difficult decisions as to how far I should take my work. Because the original video has been transferred to film, I've tried to remove anything which was added during the process of optical copying - in other words taking it back to its condition on original transmission.

The War Machines featured a couple of instances of sound effects being faded in at the wrong points during the original studio recordings. Ayres:

"It would be very easy to 'grab' a sound effect, and put it back where it's supposed to be. I haven't done it, because it was wrongly done at the time, and that's the way it should stay. All I've tried to do is correct technical defects which have occurred later with the film, I haven't corrected things which were done wrongly on the original tapes. Except in two places."

Ayres edited two instances of the original sound engineer on the serial fading the audio up and down quickly and creating uneven sound levels.

Since work on the Doctor Who DVD releases began, the frequency of these edits and revisions has increased. The earliest releases had the colour graded to appear more consistent. Later releases have had their opening and closing credits remade using modern software and Adobe fonts, untidy transitional frames have often been removed resulting in a slightly shorter running time, miscued sound effects are routinely adjusted and visual effects considered substandard are adjusted. The colour grading is often noticeably different from the broadcast originals.

For example, when recreating effects for the serial The Pirate Planet, the Team explained that "In the remade version, we took the liberty of allowing the wrench to be blasted back towards the camera at this point to help 'sell' the effect better."

Mistakes
On a number of occasions the Restoration Team's approach of, wherever possible, sourcing original film, film negatives, studio VT and audio tracks, and then reconstructing the episodes to save on a copy generation has resulted in some accidental omissions. For example, on The Time Warrior DVD, the credit caption for David Daker (Irongron) and John Carney (Bloodaxe) in episode One was omitted during the process of remaking the credit sequences. On the Trial of a Timelord DVD, the 'tractor-beam door' sound effect during the opening shot was accidentally omitted as the sequence was reconstructed from its component parts.