How do delete scenes from a mp4/mkv/etc while keeping the subtitles...

I have found a software that Deletes any scene i want from a movie & it worked like a charm.The problem is , when i drag and drop the SRT Subtitles file over the CONVERTED mp4/mkv file,the subtitles get out of order.It makes sense , i know...

So next thing i thought that i will use a software to hard-code SRT Subtitles in to the mp4 / mkv movie files & then use this software to Edit the scenes..

I saw this video on youtube of this guy explaining how to hard-code subtitles in to movie files using VLC.I followed his instructions.When i pressed START for conversion,my system started making a HUGE NOISE as if an Airplane is about to take off and the sound remains as long as the file is set on conversion , which takes around half an hour or so.

Now i have a gaming RIG and i can not bear that sound which could be damaging my Nvidia Gtx Graphics card and other hardware IN THE LONG RUN. Because i have like may be 200 or more movies & if you do the math.That means that for almost 200 times , my system would be running like that airplane and God knows what it will do to my Card :)

So,i am looking for a way to easily hard-code the subtitles and then Delete the scenes which i do not want....
What do i need to do....

I see.I would like to give you some information regarding my RIG.I removed the Stock Intel FAN (Kindly See Picture # 1 ) and got a Liquid Cooling Fan by a company named CORSAIR (See Attached Picture # 2 & 3)

This was a suggestion made to me by the Guy whom i bought my assembled RIG from.I was having some heat issues initially and my RIG was lying below my computer table which was also a casue of the overheating but i thought , the stock Cooling fan also was the cause.So,for best results and not getting worried about overheating while gaming,i bought this CORSAIR Liquid Cooling fan.The Shop guy said that my RIG can have 3 fans in Total & with this Liquid CORSAIR Liquid Cooling fan installed,i wouldn't need an other fan according to him.

Also, I do not hear that HUGE Sound during gaming or during watching HD videos online on youtube or any other website. Yes,the sound starts to increase initially when a video or website is about to be opened but the sound quickly quiets down in a few seconds.
Also,During gaming,a slight voice can be heard which is nothing compared to that sound that came during that process of hard-cording Subtitles in to a movie file.

My System Specs are :

Processor > Intel(R) Core (TM) i7 - 4790 CPU @ 3.60GHz 3.60
RAM > 16 GB
System Type > 64 Bit Operating System
Graphics Card > Nvidia GTX 960 2 GB

wasnotwas said:

You can hard code subs on mp4 with Handbrake
https://handbrake.fr/

Avidemux set to copy does lossless mp4 edits, if the cuts are on an I-frame (other edits need recode)
Avidemux - Main Page

Thank you.I just installed and used Handbrake.It was very easy to use and i didn't heard a really loud noise during the convertion process.

However,i noticed that the Output file size has increased tremendously.The Movie File size that i used had a size of 1.59 GB.Where as the converted Movie File size was 2.51 GB.

Can't i convert the file and get the same file size or perhaps slightly more file size the original File... ?

Handbrake settings suggestions -

picture tab -
anamorphic none (ie square pixels), keep aspect ratio = output file has same pixel size

video tab -
quality to R = less compression (larger filesize), quality to L = more compression (smaller filesize)
or set bitrate - R click original file > properties > details > check bitrate > set new bitrate to same value
and 2 pass, turbo 1st pass

audio -
mixdown = stereo

wasnotwas said:

Handbrake settings suggestions -

picture tab -
anamorphic none (ie square pixels), keep aspect ratio = output file has same pixel size

video tab -
quality to R = less compression (larger filesize), quality to L = more compression (smaller filesize)
or set bitrate - R click original file > properties > details > check bitrate > set new bitrate to same value
and 2 pass, turbo 1st pass

audio -
mixdown = stereo

Will convert again with these settings & let you know....