Repartition internal storage

[Wropzter]

Hello!

I managed to flash the CM 12.1 rom but I noticed that the /system partition is barely large enough (585Mb). It is so small that
I can't install the gapps package I need.

I also note that my /userdata partition is 1200Mb.
I would like to decrease the size of the userdata partition and increase the size of the system partition.
I am able to do this fine through adb shell after booting into TWRP recovery - but
the changes don't stick.

In some cases (not sure if it's when I mess up the partition table) - the partition table is simply reset
upon reboot.
In other cases - the partition table is reset - but contains duplicate partitions (as shown below)

~ # fdisk -l -u /dev/block/mmcblk0
Warning: deleting partitions after 60

Disk /dev/block/mmcblk0: 2332 MB, 2332033024 bytes
1 heads, 16 sectors/track, 284672 cylinders, total 4554752 sectors
Units = sectors of 1 * 512 = 512 bytes

              Device Boot      Start         End      Blocks  Id System
/dev/block/mmcblk0p1   *           1        1000         500  4d Unknown
Partition 1 does not end on cylinder boundary
/dev/block/mmcblk0p2            1001        1128          64  45 Unknown
Partition 2 does not end on cylinder boundary
/dev/block/mmcblk0p3            1129       10128        4500  46 Unknown
Partition 3 does not end on cylinder boundary
/dev/block/mmcblk0p4           10129     4554750     2272311   5 Extended
Partition 4 does not end on cylinder boundary
/dev/block/mmcblk0p5           10130       70129       30000  49 Unknown
/dev/block/mmcblk0p6           70131       95130       12500  50 Unknown
/dev/block/mmcblk0p7           95132       99227        2048  51 Unknown
/dev/block/mmcblk0p8           99229      105372        3072  52 Unknown
/dev/block/mmcblk0p9          105374      109469        2048  53 Unknown
/dev/block/mmcblk0p10         109471      111518        1024  54 Unknown
/dev/block/mmcblk0p11         111520      113567        1024  56 Unknown
/dev/block/mmcblk0p12         113569      131071        8751+ 55 Unknown
/dev/block/mmcblk0p13         131073      137216        3072  4a Unknown
/dev/block/mmcblk0p14         137218      143361        3072  4b Unknown
/dev/block/mmcblk0p15         143363      145410        1024  74 Unknown
/dev/block/mmcblk0p16         145412      163326        8957+ 75 Unknown
/dev/block/mmcblk0p17         163328      163839         256  76 Unknown
/dev/block/mmcblk0p18         163841      165888        1024  47 Unknown
/dev/block/mmcblk0p19         165890      167937        1024  34 Unknown
/dev/block/mmcblk0p20         167939      170498        1280  36 Unknown
/dev/block/mmcblk0p21         170500      187901        8701  71 Unknown
/dev/block/mmcblk0p22         187903      196094        4096  48 Unknown
/dev/block/mmcblk0p23         196096      196607         256  73 Unknown
/dev/block/mmcblk0p24         196609      200702        2047  26 Unknown
/dev/block/mmcblk0p25         200704     1343486      571391+ 83 Linux
/dev/block/mmcblk0p26        1343488     3749886     1203199+ 83 Linux
/dev/block/mmcblk0p27        3749888     4046846      148479+ 83 Linux
/dev/block/mmcblk0p28        4046848     4358143      155648  83 Linux
/dev/block/mmcblk0p29        4358145     4364286        3071  33 Unknown
/dev/block/mmcblk0p30        4364288     4406782       21247+ 19 Unknown
/dev/block/mmcblk0p31        4406784     4407295         256  23 Unknown
/dev/block/mmcblk0p32          10130       70129       30000  49 Unknown
/dev/block/mmcblk0p33          70131       95130       12500  50 Unknown
/dev/block/mmcblk0p34          95132       99227        2048  51 Unknown
/dev/block/mmcblk0p35          99229      105372        3072  52 Unknown
/dev/block/mmcblk0p36         105374      109469        2048  53 Unknown
/dev/block/mmcblk0p37         109471      111518        1024  54 Unknown
/dev/block/mmcblk0p38         111520      113567        1024  56 Unknown
/dev/block/mmcblk0p39         113569      131071        8751+ 55 Unknown
/dev/block/mmcblk0p40         131073      137216        3072  4a Unknown
/dev/block/mmcblk0p41         137218      143361        3072  4b Unknown
/dev/block/mmcblk0p42         143363      145410        1024  74 Unknown
/dev/block/mmcblk0p43         145412      163326        8957+ 75 Unknown
/dev/block/mmcblk0p44         163328      163839         256  76 Unknown
/dev/block/mmcblk0p45         163841      165888        1024  47 Unknown
/dev/block/mmcblk0p46         165890      167937        1024  34 Unknown
/dev/block/mmcblk0p47         167939      170498        1280  36 Unknown
/dev/block/mmcblk0p48         170500      187901        8701  71 Unknown
/dev/block/mmcblk0p49         187903      196094        4096  48 Unknown
/dev/block/mmcblk0p50         196096      196607         256  73 Unknown
/dev/block/mmcblk0p51         196609      200702        2047  26 Unknown
/dev/block/mmcblk0p52         200704     1343486      571391+ 83 Linux
/dev/block/mmcblk0p53        1343488     3749886     1203199+ 83 Linux
/dev/block/mmcblk0p54        3749888     4046846      148479+ 83 Linux
/dev/block/mmcblk0p55        4046848     4358143      155648  83 Linux
/dev/block/mmcblk0p56        4358145     4364286        3071  33 Unknown
/dev/block/mmcblk0p57        4364288     4406782       21247+ 19 Unknown
/dev/block/mmcblk0p58        4406784     4407295         256  23 Unknown
/dev/block/mmcblk0p59          10130       70129       30000  49 Unknown
/dev/block/mmcblk0p60          70131       95130       12500  50 Unknown

(Note how partition 32 and onwards are just copies of the earlier ones)

My question is, is there some part of the system that actually tries to repair/reset the partition table after I have changed it - or does TWRP simply not save the changes I do for some reason?
What part of my system might reset the partition table & why?

Thanks!