Which version of Sins are you running?  Entrenchment needs the entity.manifest to reflect what has been added to the gameinfo folder. 1.15 or less dont i believe, but there are a million things in a mod that can go wrong. Just take it a step at a time, and test after each step. 

I used to mod like for a couple hours at a shot, (im still new at this, so dont think im way experienced, just a little experienced)    And then i'd fire it up and it would crash. Well, i had NO way, haha, to figure out what went wrong. So i started changing small things, one at a time, and testing it, firing it up and seeing how it played. After that i still had problems, but they were easier to find when i knew what i had last changed.  

Start from a fresh copy if its not too much work, or take part of it out and see if it loads okie. Then add a little back at a time.  

Until it works all together and done.  

-Teal

 hope it helps

Here are some tips to help you with this:

A.) Make sure you reduced the "count" under "capitalshipinfo" in whichever "player.entity" file you changed to match the number of remaining capital ships listed in that file

B.) Make sure you didn't leave any empty newlines in place of the 4 removed capital ship entries in said Player file

Aside.) As a test, I made a tiny (1 file in a "GameInfo" folder within a "TestMod" folder within the "Sins ent 1.01 ModPath" folder, and nothing else) mod that stripped the phase of all capital ships except the battleship.  Loaded it ingame by itself, and it loaded perfectly and reduced my selection appropriately

C.) In your first post you say "i  changed the fleet size to 350". If by this you mean "I changed the remaining capital ship's fleet supply requirement = 350", then that's fine.  It causes no issues whatsoever

Aside2.) I added to my mod's GameInfo folder an edited "CAPITALSHIP_PHASEBATTLESHIP.entity" to require 350 fleet, and it worked without any issues.

D.) I have added 1 ability (with 2 supporting buffs), and 2 research subjects to my ent 1.01 mod, and here's what I had to keep in mind to make them all work:

D1.) If you add any custom descriptions/names to your custom abilities, you'll need to add a "String" folder to your "TestMod" folder; copy over the ENTRENCHMENT string file "English.str"; append your new string entries to the end (or add to the beginning); and increase the count at the top by however many entries you added.   Failure to add your strings won't crash the game, but it would give you something like "string not found" in-game instead of a name and description.

D2.) ALL new ".entity" files created solely by you (not IL) (whether abilities, buffs, frigates,capitalships,researchsubjects,etc...) must have their full names (meaning "name"+".entity") added to your own copy of the entrenchment "entity.manifest" file (this file should be placed in the root of your mod folder. meaning it is Beside the "GameInfo" and "String" folders, not within either). You get this base file from "SinsInstall\Entrenchment".  The entries do not have to be in alphabetical order (I'd insert them at the top of the file, so you can easily find them in the future).  Once their names are added to the file, increase the count at the top of the file by however many you added.

D3.) When copying and renaming existing ability/buff .entity files for use as a template in your custom files keep in mind a few things:   "Ability" files almost always point to a related "Buff" file.  You'll need to update that line of the "Ability" file to point at the new(renamed) "buff" file.   Many buffs (although not the gaussblast one) have a buffSpawner/buffTarget set of "buff" files.  The "bufftarget" entity file usually has an end condition that checks for the "buffSpawner"'s continued existence (and ends if it's no longer around). Again, update these names to the new ones you've changed them to. Otherwise you'll have affects that end immediately . It took me forever to figure out why my "disabled phasedrive" effect was ending within 1 second of applying to an enemy ship   The crazy thing was that if that ship was being affected by the original phase chargeup delay (which my affect was checking for), my affect would then "stick".

D4.) Objects etc in ent 1.01 support 5 abilities true, but starbases and capital ships can only display the buttons/icons for 4 of these.  The ramifications of this are that whatever you put in "ability:4" (which is #5) must be a passive ability (you don't need to click it for it to work) because its button/icon will be overwritten by either the starbases "upgrade-management" button, or the capital ships "ability-management" button.    For starbases, it's simply a matter of moving the passive "Phase Destabalization" ability into "ability:4", and putting your custom ability into its old spot. Capital ships that have Passives can do the same thing (move one of the passives to "ability:4", and put your new ability in the old spot).   Caps without passives though are SOL (unless you're adding a custom passive of course, then just slap that bad-boy in "ability:4" directly)

Finally, I should reiterate the great point Teal made.... make changes a little bit at a time, and load the game in between each.  This will let you know exactly what causes the issue as soon as it's introduced.

Hopefully this helps you out a bit, if you need clarification/examples for any particular detail just let me know!