I started a new game recently and played a couple of hours. The topic "little Advice" was present in the game, and there was no warning message about it. When I saved, exited, and restarted (without changing any files) I get this error message:
Master file topic 'little advice' has been deleted by 'KS_Julan_Ashlander Companion_1.3.esp'. I check the esp in the CS, and the topic is still there, not deleted. Yet loading the game, 'Little Advice' is gone.
So I test it by removing all changes to Little Advice from Julan. Load the game, and now it says Master file topic 'little advice' has been deleted by 'CITY Seyda Neen.esp'. (That's an esp I created.) Again, it has not been deleted by that esp either.
The problem with Little Advice is following the load order - KS was the first esp that touched Little Advice, then CITY Seyda Neen. So the problem is with the topic, not the esp's. I feel if I ignore the changes in CITY, it will just move down to the next esp that touched Little Advice.

Anyone have any idea why? The warning text file shows nothing else, and it did not happen when I started the game - only after saving, wxiting, and restarting - making no changes to the esp's during that time.

My loaded mods are:

GameFile0=Better Heads Bloodmoon addon.esm
GameFile1=Better Heads Tribunal addon.esm
GameFile2=Better Heads.esm
GameFile3=Bloodmoon Landscape Overhaul 1.0.esm
GameFile4=Bloodmoon.esm
GameFile5=Book Rotate.esm
GameFile6=GDR_MasterFile.esm
GameFile7=Imp Guard anticlone.esm
GameFile8=Morrowind Patch v1.6.4 (WIP).esm
GameFile9=Morrowind.esm
GameFile10=MW_Children_1_0.esm
GameFile11=Object Permanence v2.esm
GameFile12=SG-MW-ecology-BM.esm
GameFile13=Siege at Firemoth Fort.esm
GameFile14=Texture Fix - Bloodmoon 1.1.esm
GameFile15=Texture Fix 1.8.esm
GameFile16=Tribunal.esm
GameFile17=abotWhereAreAllBirdsGoing.esp
GameFile18=AEA-Compatability.esp
GameFile19=Animated Morrowind 1.0.esp
GameFile20=ASE Bloodmoon Expansion.esp
GameFile21=ASE Tribunal Expansion.esp
GameFile22=AtmosphericSoundEffects-3.0-Tribunal.esp
GameFile23=Better Bodies.esp
GameFile24=Better Clothes_v1.1.esp
GameFile25=BetterClothes_Patch.esp
GameFile26=BetterMusicSystem_v1.1.1.esp
GameFile27=Book Jackets - Combined - BookRotate.esp
GameFile28=Book Rotate - Combined.esp
GameFile29=Chargen_Revamped_v2_3.esp
GameFile30=CITY Ald Redaynia Extended COM.esp
GameFile31=CITY Ald-Ruhn.esp
GameFile32=CITY Balmora.esp
GameFile33=CITY Better Caldera COM.esp
GameFile34=CITY Dagon Fel.esp
GameFile35=CITY Ebonheart.esp
GameFile36=CITY Seyda Neen.esp
GameFile37=CITY Suran.esp
GameFile38=CITY Vivec.esp
GameFile39=Complete Armor Joints.esp
GameFile40=CPRS.esp
GameFile41=DN-GDRv1.esp
GameFile42=Elders of Vvardenfell.esp
GameFile43=EmmasKhuul.esp
GameFile44=EmmasTelMora1_0.esp
GameFile45=Guarded GhostGate.esp
GameFile46=Haunted Tombs v1.06.esp
GameFile47=horationpcenhanced12-bm.esp
GameFile48=HOUSE Bal Isra.esp
GameFile49=HOUSE Indarys Manor.esp
GameFile50=Illuminated Windows - Bloodmoon.esp
GameFile51=Illuminated Windows.esp
GameFile52=KS_Julan_Ashlander Companion_1.3.esp
GameFile53=Less_Generic_Bloodmoon.esp
GameFile54=Less_Generic_Nerevarine.esp
GameFile55=Less_Generic_Tribunal.esp
GameFile56=LGNPC_Aldruhn_v1_20.esp
GameFile57=LGNPC_Aldruhn_v1_20_suppl.esp
GameFile58=LGNPC_AldVelothi_v1_20.esp
GameFile59=LGNPC_GnaarMok_v1_10.esp
GameFile60=LGNPC_HlaOad_v1_32.esp
GameFile61=LGNPC_IndarysManor_v1_51.esp
GameFile62=LGNPC_Khuul_v2_10.esp
GameFile63=LGNPC_MaarGan_v1_20.esp
GameFile64=LGNPC_NoLore_v0_83.esp
GameFile65=LGNPC_PaxRedoran_v1_20.esp
GameFile66=LGNPC_Pelagiad_v1_22.esp
GameFile67=LGNPC_SecretMasters_v1_30.esp
GameFile68=Lgnpc_SN.esp
GameFile69=LGNPC_TelMora_v1_20.esp
GameFile70=LGNPC_TelUvirith_v1_20.esp
GameFile71=LGNPC_VivecFQ_v2_10.esp
GameFile72=LGNPC_VivecRedoran_v1_50.esp
GameFile73=LightTheWayScriptBM.esp
GameFile74=Mashed Lists.esp
GameFile75=MDP Compilation.ESP
GameFile76=Merged_Objects.esp
GameFile77=Mournhold Clockmaker 1.0.esp
GameFile78=Muck Shovel of Vivec v1.1.esp
GameFile79=npce_mwse_patch.esp
GameFile80=NX9_daedra_Additions.ESP
GameFile81=OSTAR Armor Combined.esp
GameFile82=OSTAR BM Combined.esp
GameFile83=OSTAR Books Combined.esp
GameFile84=OSTAR COM.esp
GameFile85=OSTAR Creatures Combined.esp
GameFile86=OSTAR Dark Brotherhood Combined.esp
GameFile87=OSTAR Dialogue Combined.esp
GameFile88=OSTAR Environments Combined.esp
GameFile89=OSTAR Fixes and Tweaks.esp
GameFile90=OSTAR Indarys.esp
GameFile91=OSTAR Items Combined.esp
GameFile92=OSTAR Keys Combined.esp
GameFile93=OSTAR NPC Combined.esp
GameFile94=OSTAR Quest Fixes Combined.esp
GameFile95=OSTAR Quests Combined.esp
GameFile96=OSTAR Races and Classes.esp
GameFile97=OSTAR Reality Combined.esp
GameFile98=OSTAR Redoran Expansion.esp
GameFile99=OSTAR Signs Combined.esp
GameFile100=OSTAR Sixth House Combined.esp
GameFile101=OSTAR Sounds Combined.esp
GameFile102=OSTAR Tribunal Combined.esp
GameFile103=OSTAR Weapons Combined.esp
GameFile104=PC VOICE COMPLETEv1.8.esp
GameFile105=SeriousWeather_BM_v1_00.esp
GameFile106=SG-MW-ecology-BM-plugin.esp
GameFile107=South Wall.ESP
GameFile108=Starfires NPC Additions ver-1.11.esp
GameFile109=SW_ASE_ADDON.esp
GameFile110=The Neverhalls.esp
GameFile111=TLM - Complete.esp
GameFile112=TravelingMerchants_v2.2.esp
GameFile113=UUMPP LGNPC Fixes.esp
GameFile114=Vality's Ascadian Isles Addon.esp
GameFile115=Vality's Bitter Coast Addon.esp
GameFile116=VGREETINGS Combined.esp
GameFile117=Vos Expansion.ESP
GameFile118=WAKIM Balance and Gameplay.esp
GameFile119=Westly's Dark Elf Male Headpack.esp
GameFile120=WolfComp_ver3_0.esp
GameFile121=GOTYMinImpactSomeMPP.esm