How about the following:
Starter letters SLT
WATERLINES becomes SATELLITES, giving WRN
VEGETABLES becomes RENEWABLES, giving VGT
DEFECATING becomes VEGETATING, giving DFC
RESILIENCY becomes DEFICIENCY, giving RSL
UNDEFEATED becomes UNRELEASED, giving DFT
LASCIVIOUS becomes FASTIDIOUS, giving LCV
WOMANIZING becomes VOCALIZING, giving WMN
FEATHERBED becomes WEATHERMEN, giving FBD
REORIENTED becomes BEFRIENDED, giving ROT
COMMENTERS becomes TORMENTORS, giving CME as the final three letters
Some notes on my working (entirely trial and error):
FEATHERBED --> WEATHERMEN came first, since I didn't think much could change in this word and remain a legal word. I got quite fixated on this having to be correct, so was very pleased when I spotted that the resulting BFD led to changing REORIENTED to BEFRIENDED. The TOR providing me with the change from COMMENTERS to TORMENTORS came next, though it took a while longer to spot this. This left me with a CME I was struggling to substitute into another word...
The WMN to enable the FEATHERBED change had to come from WOMANIZING. What else could legitimately make a word of the pattern _O_A_IZING? Well, once I spotted FASTIDIOUS --> LASCIVIOUS, the resulting VCL neatly enabled VOCALIZING. How to get the FTD to enable this? Well, that had to come from either FEATHERBED (impossible), DEFECATING or UNDEFEATED. I could not be sure yet.
Another pairing which seemed nicely matched was a possible change from RESILIENCY to DEFICIENCY, freeing up RSL. To do this required the DFC from DEFECATING, giving a word of the form _E_E_ATING. This also meant that FEATHERBED's FTD had to come from UNDEFEATED, giving a word of the form UN_E_EA_ED or UNDE_EA_E_.
I turned my attention to VEGETABLES. There are not many words which begin with VEGE or contain EGE, in my experience. This meant that likely the V and/or G would have to change. Since the ABLES suffix is fairly common, I concentrated on words of the form _E_E_ABLES. This freed up a VGT to create VEGETATING as the step before DEFECATING. What could go in the gaps? After several failed attempts looking for letters available in unused words I hit upon RENEWABLES, using the RNW from WATERLINES.
So what could WATERLINES become without RNW? Something of the form _ATE_LI_ES... I entertained the possibility of SATELLITES as one option, but the required SLT was not available in another word...
This left me two 'chunks':
WATERLINES + SLT --> SATELLITES + RNW
VEGETABLES + RNW --> RENEWABLES + VGT
DEFECATING + VGT --> VEGETATING + DFC
RESILIENCY + DFC --> DEFICIENCY + RSL
UNDEFEATED + ??? --> UN?E?EA?ED or UNDE?EA?E? + DFT
LASCIVIOUS + DFT --> FASTIDIOUS + LCV
WOMANIZING + VCL --> VOCALIZING + WMN
FEATHERBED + WMN --> WEATHERMEN + FBD
REORIENTED + FBD --> BEFRIENDED + ROT
COMMENTERS + ROT --> TORMENTORS + CME
I tried to spot a connection between these two chunks for AAAAGES, teetering on the verge of adding UNRESEALED into the dictionary. Some minutes later, the facepalm moment struck: UNRELEASED! So the starter letters had to be SLT and the leftovers CME.
Phew! Definitely time for bed...